[REVIEW]: rmap: An R package to plot and compare tabular data on customizable maps across scenarios and time

whedon commented 2 years ago

Submitting author: !--author-handle-->@zarrarkhan@hugoledoux<!--end-editor-- Reviewers: @CamilleMorlighem, @maczokni Archive: 10.5281/zenodo.7085969

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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

@CamilleMorlighem & @maczokni, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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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 ✨

Review checklist for @CamilleMorlighem

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@zarrarkhan) 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

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 and who the target audience is?
[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?

Review checklist for @maczokni

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] #4016

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@zarrarkhan) 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

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 and who the target audience is?
[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?

hugoledoux commented 2 years ago

@editorialbot check references

hugoledoux commented 2 years ago

@zarrarkhan thanks, everything looks good in the paper and the docs.

I have 2 small comments/questions:

what are ggplot "arguments"? (l.53+56). I don't use ggplot and I wouldn't know what you're referring to, perhaps just use "functionalities"?
the reference for Pebesma simple feature has the name of the journal missing, and then the github repo is cited. To fix.

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/s10113-021-01775-1 is OK
- 10.1088/1748-9326/ac046c is OK
- 10.18637/jss.v084.i06 is OK
- 10.21105/joss.00054 is OK
- 10.32614/RJ-2011-006 is OK
- 10.1007/b106573 is OK
- 10.1029/2020EF001970 is OK
- 10.5194/gmd-12-677-2019 is OK
- 10.5334/jors.292 is OK

MISSING DOIs

- Errored finding suggestions for "Package ‘GISTools’", please try later
- Errored finding suggestions for "QGIS", please try later
- Errored finding suggestions for "S classes and methods for spatial data: the sp pac...", please try later
- Errored finding suggestions for "Simple features for R: standardized support for sp...", please try later
- Errored finding suggestions for "choroplethr: Simplify the Creation of Choropleth M...", please try later
- Errored finding suggestions for "ArcGIS", please try later
- Errored finding suggestions for "GRASS GIS graphical user interface", please try later
- Errored finding suggestions for "ggplot2", please try later
- Errored finding suggestions for "rfasst: An R tool to estimate air pollution impact...", please try later

INVALID DOIs

- None

zarrarkhan commented 2 years ago

@zarrarkhan thanks, everything looks good in the paper and the docs.

I have 2 small comments/questions:

what are ggplot "arguments"? (l.53+56). I don't use ggplot and I wouldn't know what you're referring to, perhaps just use "functionalities"?

the reference for Pebesma simple feature has the name of the journal missing, and then the github repo is cited. To fix.

Thanks @hugoledoux. Both comments addressed as follows in latest push: http://res.cloudinary.com/hkvhhndao/image/upload/v1663018510/xpwhvwopcw7c7jm9q3ir.pdf

Updated to say ggplot functionality and ggplot chart objects
Reference fixed with full journal name added (The R Journal) as well as correct link to article.

Let me know if you have additional comments/edits for me to make. Best Zarrar

hugoledoux commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

hugoledoux commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/s10113-021-01775-1 is OK
- 10.1088/1748-9326/ac046c is OK
- 10.18637/jss.v084.i06 is OK
- 10.21105/joss.00054 is OK
- 10.32614/RJ-2011-006 is OK
- 10.1007/b106573 is OK
- 10.1029/2020EF001970 is OK
- 10.5194/gmd-12-677-2019 is OK
- 10.5334/jors.292 is OK

MISSING DOIs

- Errored finding suggestions for "QGIS", please try later
- Errored finding suggestions for "S classes and methods for spatial data: the sp pac...", please try later
- Errored finding suggestions for "Simple features for R: standardized support for sp...", please try later
- Errored finding suggestions for "choroplethr: Simplify the Creation of Choropleth M...", please try later
- Errored finding suggestions for "ArcGIS", please try later
- Errored finding suggestions for "GRASS GIS graphical user interface", please try later
- Errored finding suggestions for "ggplot2", please try later
- Errored finding suggestions for "rfasst: An R tool to estimate air pollution impact...", please try later

INVALID DOIs

- None

hugoledoux commented 2 years ago

Thanks, all looks good.

At this point 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 accepting the submission.

zarrarkhan commented 2 years ago

@hugoledoux

Addressed as follows:

Tagged version of software: v1.0.2 https://github.com/JGCRI/rmap/releases/tag/v1.0.2
Archived on Zenodo: https://doi.org/10.5281/zenodo.7080178
Metadata checked with correct title matching paper title and all author names with ORCID IDs from paper.
DOI: 10.5281/zenodo.7080178

Please let me know if you need anything else.

Best

Zarrar

hugoledoux commented 2 years ago

one tiny thing to fix: Tomas Wild is Tom Wild on Zenodo. The names have to be exactly the same, edit one to harmonise please.

zarrarkhan commented 2 years ago

@hugoledoux

oops, sorry about that. Thanks for catching that! Updated and minted again:

Tagged version of software: v1.0.3 https://github.com/JGCRI/rmap/releases/tag/v1.0.3
Archived on Zenodo: https://zenodo.org/record/7082820#.YyNRrXbMJaQ
Metadata checked with correct title matching paper title and all author names with ORCID IDs from paper.
DOI: 10.5281/zenodo.7082820

Best

Zarrar

hugoledoux commented 2 years ago

@editorialbot set 10.5281/zenodo.7082820 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.7082820

hugoledoux commented 2 years ago

@editorialbot set v1.0.3 as version

editorialbot commented 2 years ago

Done! version is now v1.0.3

hugoledoux commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

hugoledoux commented 2 years ago

Congraluations @zarrarkhan and team 🎉

It's been a not so simple journey to get there, but I believe the package is better and I hope it'll benefit others. Thanks @maczokni and @CamilleMorlighem for your thorough review and for testing the code!

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3531, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 2 years ago

Hi @zarrarkhan - I'm the AEiC on duty this week, and have proofread your paper. Please merge https://github.com/JGCRI/rmap/pull/92 for some very minor changes in it.

It appears https://doi.org/10.1002/wics.147 is a DOI for the Wickham reference. If you agree, please add it. Similar, I think at least a URL is needed for Brunsdon & Chen.

Once these are done, we can move to acceptance and publication.

zarrarkhan commented 2 years ago

@danielskatz @hugoledoux

Thank you so much for all your comments and edits. We agree that the review process has been very helpful and we feel much more confident in the usefulness of the software for multiple users. Updated and released in v1.0.4 with following changes:

Wheadon preview: http://res.cloudinary.com/hkvhhndao/image/upload/v1663333163/oj1b28zu3aml6r9nb4zx.pdf
Pull request https://github.com/JGCRI/rmap/pull/92 Merged
DOI for the Wickham reference added: https://doi.org/10.1002/wics.147
Brunsdon & Chen reference removed since it is no longer available on CRAN and does not look like it is being maintained.

Details for latest release

Tagged version of software: v1.0.5 https://github.com/JGCRI/rmap/releases/tag/v1.0.5
Archived on Zenodo: https://zenodo.org/record/7085969#.YyR2HXbMJaQ
Metadata checked with correct title matching paper title and all author names with ORCID IDs from paper.
DOI: 10.5281/zenodo.7085969

Hope we caught everything!

Best

Zarrar

danielskatz commented 2 years ago

@editorialbot set v1.0.5 as version

editorialbot commented 2 years ago

Done! version is now v1.0.5

danielskatz commented 2 years ago

@editorialbot set 10.5281/zenodo.7085969 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.7085969

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

:warning: Error prepararing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value 'https://doi.org/10.1002/wics.147' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

danielskatz commented 2 years ago

@zarrarkhan - note that the new DOI should be doi = {10.1002/wics.147}, instead of doi = { https://doi.org/10.1002/wics.147},

You do not need to generate a new version or a new archive for this, since it will only be a change in the paper, which is not required to be in the archived repo, but if you want to, you can.

zarrarkhan commented 2 years ago

@danielskatz oops. Sorry about that. I've changed this in paper.bib which is merged into master now. I won't create a new version. Is that okay?

danielskatz commented 2 years ago

should be - let's see :)

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3534, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/s10113-021-01775-1 is OK
- 10.1088/1748-9326/ac046c is OK
- 10.18637/jss.v084.i06 is OK
- 10.21105/joss.00054 is OK
- 10.32614/RJ-2011-006 is OK
- 10.1007/b106573 is OK
- 10.1002/wics.147 is OK
- 10.1029/2020EF001970 is OK
- 10.5194/gmd-12-677-2019 is OK
- 10.5334/jors.292 is OK

MISSING DOIs

- 10.32614/rj-2018-009 may be a valid DOI for title: Simple features for R: standardized support for spatial vector data.

INVALID DOIs

- None

danielskatz commented 2 years ago

sorry @zarrarkhan - there is one more change needed - for the first Pebesma reference, please add doi = {10.32614/RJ-2018-009}, rather than the URL that is there now.

zarrarkhan commented 2 years ago

no worries! Done and merged into main. Happy to make any other changes as needed.

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3535, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/s10113-021-01775-1 is OK
- 10.1088/1748-9326/ac046c is OK
- 10.18637/jss.v084.i06 is OK
- 10.21105/joss.00054 is OK
- 10.32614/RJ-2011-006 is OK
- 10.1007/b106573 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1002/wics.147 is OK
- 10.1029/2020EF001970 is OK
- 10.5194/gmd-12-677-2019 is OK
- 10.5334/jors.292 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3536
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04015
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 2 years ago

Congratulations to @zarrarkhan (Zarrar Khan) ad co-authors!!

And thanks to @CamilleMorlighem and @maczokni for reviewing, and to @hugoledoux for editing! We couldn't do this without you.

editorialbot commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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zarrarkhan commented 2 years ago

@danielskatz @hugoledoux @maczokni @CamilleMorlighem Thanks to all of you for the great review and very helpful feedback. We appreciate it very much! Best Zarrar

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