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

editorialbot commented 8 months ago

Submitting author: !--author-handle-->@realxinzhao@hugoledoux<!--end-editor-- Reviewers: @klau506, @HenriKajasilta Archive: 10.5281/zenodo.10967067

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

editorialbot commented 8 months ago

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:

@editorialbot generate pdf

editorialbot commented 8 months ago

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

editorialbot commented 8 months ago

Wordcount for paper.md is 3161

editorialbot commented 8 months ago

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

editorialbot commented 8 months ago

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

klau506 commented 8 months ago

Review checklist for @klau506

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/JGCRI/gcamfaostat?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[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?

HenriKajasilta commented 8 months ago

Review checklist for @HenriKajasilta

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/JGCRI/gcamfaostat?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[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?

klau506 commented 8 months ago

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 commented 8 months ago

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 commented 8 months ago

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

realxinzhao commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

realxinzhao commented 8 months ago

@editorialbot commands

editorialbot commented 8 months ago

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

realxinzhao commented 8 months ago

@editorialbot check repository

editorialbot commented 8 months ago

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

editorialbot commented 8 months ago

Paper file info:

📄 Wordcount for paper.md is 2229

✅ The paper includes a Statement of need section

editorialbot commented 8 months ago

License info:

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

realxinzhao commented 8 months ago

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)

realxinzhao commented 7 months ago

@editorialbot generate pdf

realxinzhao commented 7 months ago

@editorialbot check repository

editorialbot commented 7 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.19 s (1135.2 files/s, 448094.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                             24              0              0          47583
HTML                           119           4095            389          16383
R                               45           2031           3247           6885
CSS                              4            152             57            655
Rmd                              6            293            560            416
TeX                              1              6              0            393
XML                              1              0              0            360
YAML                             6             45             11            293
JavaScript                       4             64             32            264
Markdown                         3             83              0            163
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           214           6769           4297          73406
-------------------------------------------------------------------------------

Commit count by author:

    78  Zhao, Xin
    11  realxinzhao
     8  Xin Zhao
     1  Xin

editorialbot commented 7 months ago

Paper file info:

📄 Wordcount for paper.md is 1473

✅ The paper includes a Statement of need section

editorialbot commented 7 months ago

License info:

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

editorialbot commented 7 months ago

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

realxinzhao commented 7 months ago

Dear @hugoledoux, @klau506 and @hugoledoux,

Following suggestions from @hugoledoux, the paper length is greatly reduced. It seems the 1473 word count by the bot was a count in the md file and it included captions, acknowledgment, and url links. Per our check, the word count in the pdf is about 1200 words and even shorter if not accounting for in-text citations. Will this be okay? Thank you!

Best, Xin

klau506 commented 7 months ago

Dear @realxinzhao and @hugoledoux,

Thanks for going through all the suggestions and improving the already very complete documentation. I followed the installation procedure of gcamfaostat again and everything worked fine. The authors have done a very nice job in setting up this package to improve agronomic data management, especially in the GCAM model. I do not have anything else to add, but I will be happy to check other items if you wish.

Best, Clàudia

editorialbot commented 7 months ago

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
- 10.1038/s41467-024-46575-3 is OK
- 10.1038/sdata.2016.18 is OK
- doi10.1038/sdata.2016.18 is OK

MISSING DOIs

- No DOI given, and none found for title: FAOSTAT AgLU data Archive GCAMv7
- No DOI given, and none found for title: FAOSTAT Database
- No DOI given, and none found for title: Core Model Proposal# 360: GCAM agriculture and lan...
- No DOI given, and none found for title: gcamdata: An R package for preparation, synthesis,...

INVALID DOIs

- None

realxinzhao commented 7 months ago

@klau506 Thank you so much for the careful review and checking of the package as well as the paper. They both improved significantly as a result of your comments and suggestions!

realxinzhao commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

realxinzhao commented 7 months ago

BTW, I updated all doi in the paper. Two references, FAOSTAT data and a report, didn't have doi. But URL is added. Thanks!

HenriKajasilta commented 7 months ago

Hi @realxinzhao and @hugoledoux ,

I have reviewed the package code and documentation once more, and it seems that everything is now working as expected. Thank you for looking at the suggestions and improving the functionality. The authors have done a good job with the package and I don’t have any new suggestions to make.

realxinzhao commented 7 months ago

@HenriKajasilta Thank you so much for carefully reviewing and checking the package and the paper. Both the package and the paper have been improved significantly as a result of the great comments and suggestions!

hugoledoux commented 7 months ago

I was on holidays and now back at work. I'll process the paper in the coming days.

@realxinzhao the length of the paper is fine as is, no worries.

hugoledoux commented 7 months ago

@editorialbot check references

editorialbot commented 7 months ago

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

OK DOIs

- 10.5281/zenodo.8260225 is OK
- 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/s41467-024-46575-3 is OK
- 10.1038/sdata.2016.18 is OK

MISSING DOIs

- No DOI given, and none found for title: FAOSTAT Database
- No DOI given, and none found for title: Core Model Proposal# 360: GCAM agriculture and lan...

INVALID DOIs

- 0.5334/jors.232 is INVALID

hugoledoux commented 7 months ago

OK, I proof-read the paper and all is good, I couldn't find a typo or a weird sentence. Nice clear paper 👍

Could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) 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 recommending acceptance of the submission.

editorialbot commented 7 months ago

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

OK DOIs

- 10.5281/zenodo.8260225 is OK
- 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.232 is OK
- 10.5334/jors.266 is OK
- 10.5334/jors.208 is OK
- 10.1038/s41467-024-46575-3 is OK
- 10.1038/sdata.2016.18 is OK

MISSING DOIs

- No DOI given, and none found for title: FAOSTAT Database
- No DOI given, and none found for title: Core Model Proposal# 360: GCAM agriculture and lan...

INVALID DOIs

- None

realxinzhao commented 7 months ago

@hugoledoux Thank you so much!

The released version on GitHub is gcamfaostat v1.0.0: https://github.com/JGCRI/gcamfaostat/releases/tag/v1.0.0 The Zenodo archive is created with metadata updated: https://zenodo.org/records/10967067 The DOI is 10.5281/zenodo.10967067

Please let us know if we can provide more information. Thanks!

realxinzhao commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

hugoledoux commented 6 months ago

Sorry for the delay @realxinzhao

There is one issue: the names on the paper are not the exact same as those on zenodo archiving: Christopher R. Vernon + Katherine V. Calvin + Marshall A. Wise are different, and we want them to be the same. You can modify either the paper or zenodo metadata so that they match.

The rest is fine!

realxinzhao commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

realxinzhao commented 6 months ago

Thank you, @hugoledoux! Good catch. The names on the paper is fixed now to match zenodo.

hugoledoux commented 6 months ago

no: "ChrisT Vernon" vs "Chris Vernon" 🫤

realxinzhao commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

realxinzhao commented 6 months ago

@hugoledoux 👍 Oops, sorry about that. It is corrected now. Thank you so much!

openjournals / joss-reviews