[REVIEW]: wdpar: Interface to the World Database on Protected Areas #4594

editorialbot · 2022-07-19T20:26:19Z

Submitting author: @jeffreyhanson (Jeffrey Hanson)
Repository: https://github.com/prioritizr/wdpar
Branch with paper.md (empty if default branch):
Version: v1.3.3.2
Editor: @martinfleis
Reviewers: @Jo-Schie, @DrMattG
Archive: 10.5281/zenodo.7195676

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2ce897960e750fee08a3df84e4d52c3b"><img src="https://joss.theoj.org/papers/2ce897960e750fee08a3df84e4d52c3b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2ce897960e750fee08a3df84e4d52c3b/status.svg)](https://joss.theoj.org/papers/2ce897960e750fee08a3df84e4d52c3b)

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

@Jo-Schie & @DrMattG, 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 @martinfleis 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 @DrMattG

📝 Checklist for @Jo-Schie

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-07-19T20:26:20Z

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:

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

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editorialbot · 2022-07-19T20:26:22Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1123.7 files/s, 163951.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            19            634             68           3589
R                               23             79            978           1293
Markdown                         5            206              0            509
CSS                              3             98             52            442
YAML                             6             67              8            363
JavaScript                       3             64             32            256
TeX                              1             20              0            194
Rmd                              3            121            242            158
make                             1             21              0             67
XML                              1              0              0             57
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                            66           1310           1381           6939
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-07-19T20:26:23Z

Wordcount for paper.md is 653

editorialbot · 2022-07-19T20:26:25Z

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

OK DOIs

- 10.1111/brv.12044 is OK
- 10.1371/journal.pone.0188681 is OK
- 10.1111/cobi.12095 is OK
- 10.1111/conl.12158 is OK
- 10.1038/nature13947 is OK
- 10.1016/j.gecco.2018.e00424 is OK
- 10.1038/s41559-021-01528-7 is OK
- 10.1038/s41559-019-0869-3 is OK
- 10.1016/j.scitotenv.2021.152316 is OK
- 10.3390/biology11040552 is OK
- 10.3390/biology10030195 is OK
- 10.1016/j.gecco.2020.e01247 is OK
- 10.1111/1365-2664.13718 is OK
- 10.3390/plants10050992 is OK
- 10.4404/hystrix-00489-2021 is OK
- 10.1038/s41893-021-00815-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-07-19T20:27:36Z

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

martinfleis · 2022-07-19T20:43:40Z

👋🏼 @jeffreyhanson, @Jo-Schie & @DrMattG this is the review thread for the paper. All of our communications will happen here from now on.

All reviewers should create checklists with the JOSS requirements using the command @editorialbot generate my checklist. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues (and small pull requests if needed) on the software repository. When doing so, please mention #4594 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks, feel free to start whenever it works for you. Please let me know if any of you require significantly more time. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@martinfleis) if you have any questions/concerns.

DrMattG · 2022-07-21T17:47:07Z

Review checklist for @DrMattG

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 https://github.com/prioritizr/wdpar?
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 (@jeffreyhanson) 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: 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?

Jo-Schie · 2022-07-23T07:17:29Z

Review checklist for @Jo-Schie

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 https://github.com/prioritizr/wdpar?
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 (@jeffreyhanson) 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: 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?

Jo-Schie · 2022-07-23T08:17:08Z

Check installation for:

Ubuntu/Linux
MacOS
Windows @DrMattG : Do you have a Windows machine where you could test installation? @martinfleis : do we both need to test installation on all platforms or can we have a division of labor somehow? I work mostly with linux but I'm also able to check on MacOS.

DrMattG · 2022-07-23T08:42:19Z

I have windows - so can test installation

martinfleis · 2022-07-23T09:05:06Z

@Jo-Schie If you have a possibility to check on more OS it would be welcome to do so, but don't feel obliged to test on all.

Jo-Schie · 2022-07-23T09:18:53Z

@martinfleis : I opened a new issue in the repo. Is the link there enough or do I need to link from here to there as well? As far as I can see, the issue appears anyway in this threat...

martinfleis · 2022-07-23T09:19:39Z

Yeah, link there is enough. Thanks!

Jo-Schie · 2022-07-23T09:31:30Z

@Jo-Schie If you have a possibility to check on more OS it would be welcome to do so, but don't feel obliged to test on all.

AFAIK all packages on CRAN are going through some automated installation checks anyways before publication...not sure if this is cross-Plattform though.

jeffreyhanson · 2022-09-03T15:32:13Z

Hi @DrMattG, I just wanted to follow up and ask if there was anything I could do to help you complete the review? I'd be happy to answer any questions if you're experiencing any issues with installing the package or using any of the functions?

jeffreyhanson · 2022-09-03T15:36:51Z

Sorry, I forgot to respond about the operating systems checks. @Jo-Schie is correct - CRAN does ineeded run automated checks. Briefly, these checks include installation checks, a range of code and documentation checks, and unit tests. They are run on several platforms including Debian, Windows, Fedora, and macOS (including on M1 Macs) (see here for platforms: https://cran.r-project.org/web/checks/check_flavors.html). As you can see here (https://cran.r-project.org/web/checks/check_results_wdpar.html), the package passes all of these checks across all platforms.

jeffreyhanson · 2022-10-03T15:02:50Z

Massive thank you to @Jo-Schie and @DrMattG for making the time to review this submission. Their feedback was extremely helpful for improving the package and manuscript! I think I've fully addressed all of their comments now - but please correct me if I've got this wrong - so what should I do next?

martinfleis · 2022-10-13T11:53:22Z

@editorialbot check references

editorialbot · 2022-10-13T11:55:33Z

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

OK DOIs

- 10.1111/brv.12044 is OK
- 10.1371/journal.pone.0188681 is OK
- 10.1111/cobi.12095 is OK
- 10.1111/conl.12158 is OK
- 10.1038/nature13947 is OK
- 10.1016/j.gecco.2018.e00424 is OK
- 10.1038/s41559-021-01528-7 is OK
- 10.1038/s41559-019-0869-3 is OK
- 10.1016/j.scitotenv.2021.152316 is OK
- 10.3390/biology11040552 is OK
- 10.3390/biology10030195 is OK
- 10.1016/j.gecco.2020.e01247 is OK
- 10.1111/1365-2664.13718 is OK
- 10.3390/plants10050992 is OK
- 10.4404/hystrix-00489-2021 is OK
- 10.1038/s41893-021-00815-2 is OK
- 10.1126/science.aac9180 is OK
- 10.5281/zenodo.4601607 is OK
- 10.5281/zenodo.256882 is OK
- 10.32614/RJ-2018-009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

martinfleis · 2022-10-13T11:57:12Z

Thank you all! I made sure all is checked as is supposed to based on the discussions.

@jeffreyhanson The submission is now almost ready to be published.

The next steps you need to do now:

Make a new tagged release (or let me know if the latest one contains all the changes) of the software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service
Check that the archival deposit (e.g., in Zenodo) has the correct metadata. In particular, the title and author list should be identical to those of the paper.
Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

jeffreyhanson · 2022-10-13T22:30:26Z

Awesome - thanks so much @martinfleis, @DrMattG, and @Jo-Schie!

@martinfleis, I've created a tagged release (see https://github.com/prioritizr/wdpar/releases/tag/v1.3.3.2) and archived this on Zenodo (see https://doi.org/10.5281/zenodo.7195676). I also have edited the metadata so that the author list and title are identical to that of the paper. Please let me know if there's anything else I can do top help?

jeffreyhanson · 2022-10-23T06:41:35Z

@martinfleis, just to follow up, I think I've completed all those steps (see post above for release and DOI) - is there anything else I need to do?

martinfleis · 2022-10-24T09:22:01Z

@editorialbot set v1.3.3.2 as version

editorialbot · 2022-10-24T09:22:02Z

Done! version is now v1.3.3.2

martinfleis · 2022-10-24T09:22:56Z

@editorialbot set 10.5281/zenodo.7195676 as archive

editorialbot · 2022-10-24T09:22:58Z

Done! Archive is now 10.5281/zenodo.7195676

martinfleis · 2022-10-24T09:24:38Z

@editorialbot generate pdf

editorialbot · 2022-10-24T09:25:52Z

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

martinfleis · 2022-10-24T09:31:31Z

@editorialbot recommend-accept

editorialbot · 2022-10-24T09:31:32Z

Attempting dry run of processing paper acceptance...

martinfleis · 2022-10-24T09:32:01Z

Thank you @jeffreyhanson! I'm going to hand this over now to the associate EiC for the final steps.

editorialbot · 2022-10-24T09:33:05Z

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

OK DOIs

- 10.1111/brv.12044 is OK
- 10.1371/journal.pone.0188681 is OK
- 10.1111/cobi.12095 is OK
- 10.1111/conl.12158 is OK
- 10.1038/nature13947 is OK
- 10.1016/j.gecco.2018.e00424 is OK
- 10.1038/s41559-021-01528-7 is OK
- 10.1038/s41559-019-0869-3 is OK
- 10.1016/j.scitotenv.2021.152316 is OK
- 10.3390/biology11040552 is OK
- 10.3390/biology10030195 is OK
- 10.1016/j.gecco.2020.e01247 is OK
- 10.1111/1365-2664.13718 is OK
- 10.3390/plants10050992 is OK
- 10.4404/hystrix-00489-2021 is OK
- 10.1038/s41893-021-00815-2 is OK
- 10.1126/science.aac9180 is OK
- 10.5281/zenodo.4601607 is OK
- 10.5281/zenodo.256882 is OK
- 10.32614/RJ-2018-009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-10-24T09:33:41Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3639, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

jeffreyhanson · 2022-10-24T22:57:01Z

Brilliant - thank you very much @martinfleis!

kthyng · 2022-10-25T14:13:47Z

Everything looks great!

kthyng · 2022-10-25T14:13:50Z

@editorialbot accept

editorialbot · 2022-10-25T14:13:52Z

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

editorialbot · 2022-10-25T14:16:12Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-10-25T14:16:13Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.04594 joss-papers#3647
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04594
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2022-10-25T14:20:33Z

Congrats on your new publication @jeffreyhanson! Many thanks to editor @martinfleis and reviewers @Jo-Schie and @DrMattG for your time, hard work, and expertise!!

editorialbot · 2022-10-25T14:20:35Z

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

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editorialbot added Makefile R review TeX labels Jul 19, 2022

editorialbot assigned martinfleis Jul 19, 2022

editorialbot mentioned this issue Jul 19, 2022

[PRE REVIEW]: wdpar: Interface to the World Database on Protected Areas #4436

Closed

Jo-Schie mentioned this issue Jul 23, 2022

JOSS Review: Improve documentation on geo-processing steps and its effects on the original geometries prioritizr/wdpar#53

Closed

6 tasks

Jo-Schie mentioned this issue Jul 23, 2022

JOSS Review: Improve Statement of need / description of use-cases prioritizr/wdpar#54

Closed

This was referenced Sep 5, 2022

JOSS Review - Add links to references cited in README prioritizr/wdpar#58

Closed

JOSS Review warning about out of date local data prioritizr/wdpar#59

Closed

editorialbot added the Track: 6 (ESE) Earth Sciences and Ecology label Sep 10, 2022

This was referenced Sep 21, 2022

JOSS Review: Add small POC about Performance claims prioritizr/wdpar#61

Closed

JOSS Review: Add statement about state of the field prioritizr/wdpar#62

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 24, 2022

editorialbot added accepted published Papers published in JOSS labels Oct 25, 2022

kthyng closed this as completed Oct 25, 2022

editorialbot mentioned this issue Aug 22, 2024

[PRE REVIEW]: ccviR: an R package and Shiny app to implement the NatureServe Climate Change Vulnerability Index #7097

Closed

editorialbot mentioned this issue Sep 17, 2024

[PRE REVIEW]: harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats #7135

Closed

[REVIEW]: wdpar: Interface to the World Database on Protected Areas #4594

[REVIEW]: wdpar: Interface to the World Database on Protected Areas #4594

Comments

editorialbot commented Jul 19, 2022 • edited Loading

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Reviewer instructions & questions

Checklists

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martinfleis commented Jul 19, 2022

DrMattG commented Jul 21, 2022 • edited Loading

Review checklist for @DrMattG

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Jo-Schie commented Jul 23, 2022 • edited by martinfleis Loading

Review checklist for @Jo-Schie

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Jo-Schie commented Jul 23, 2022 • edited Loading

DrMattG commented Jul 23, 2022

martinfleis commented Jul 23, 2022

Jo-Schie commented Jul 23, 2022

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Jo-Schie commented Jul 23, 2022

jeffreyhanson commented Sep 3, 2022

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jeffreyhanson commented Oct 3, 2022

martinfleis commented Oct 13, 2022

editorialbot commented Oct 13, 2022

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editorialbot commented Jul 19, 2022 •

edited

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Jo-Schie commented Jul 23, 2022 •

edited by martinfleis

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