[REVIEW]: RCzechia: Spatial Objects of the Czech Republic

[editorialbot]

Submitting author: @jlacko (Jindra Lacko)
Repository: https://github.com/jlacko/RCzechia
Branch with paper.md (empty if default branch): master
Version: v1.10.2
Editor: @martinfleis
Reviewers: @nickbearman, @paleolimbot
Archive: 10.5281/zenodo.7665574

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/28cb98d1d05835ef1e54466c29dc46ab"><img src="https://joss.theoj.org/papers/28cb98d1d05835ef1e54466c29dc46ab/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/28cb98d1d05835ef1e54466c29dc46ab/status.svg)](https://joss.theoj.org/papers/28cb98d1d05835ef1e54466c29dc46ab)

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

@nickbearman & @paleolimbot, 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 @nickbearman

📝 Checklist for @paleolimbot

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.18 s (379.9 files/s, 21894.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               55            555            825           1376
Markdown                         4            163              0            283
TeX                              1             27              0            205
YAML                             4             24             11            107
Dockerfile                       1             11             10             53
HTML                             1              1              0             15
Bourne Shell                     1              1              2              8
JSON                             2              0              0              2
Rmd                              1            100            255              0
-------------------------------------------------------------------------------
SUM:                            70            882           1103           2049
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1106

[editorialbot]

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

OK DOIs

- 10.1038/s41598-021-02545-z is OK
- 10.25225/jvb.21016 is OK
- 10.32614/RJ-2018-009 is OK
- 10.21105/joss.02948 is OK
- 10.5281/ZENODO.4317946 is OK
- 10.1007/s10109-020-00336-0 is OK
- 10.2307/1218258 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[martinfleis]

👋🏼 @jlacko, @nickbearman, @paleolimbot 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.

As you know, 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 #5082 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.

Given the nature of the paper, it would also be great if you can compare its functionality to previously published packages like rgugik for Polish data or tigris for the US.

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

Thanks!

[nickbearman]

Review checklist for @nickbearman

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/jlacko/RCzechia?
• 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 (@jlacko) 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?

[nickbearman]

@jlacko I have added quite a few issues above - feel free to ask questions if they are not clear. Thanks for all of your work with this :-)

[nickbearman]

Re License jlacko/RCzechia#55 there seems to be a conflict between CRAN's license requirements and JOSS's license requirements. Personally I would say I am fine with how @jlacko has approached this, but I would also like:
a) a second opinion from another reviewer
and/or
b) a view from @martinfleis

[nickbearman]

@editorialbot generate pdf

[editorialbot]

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

[martinfleis]

there seems to be a conflict between CRAN's license requirements and JOSS's license requirements

This solution seems to be a standard way of dealing with the issue of having a human-readable License file JOSS requires as well as CRAN version. So I am fine with the solution. Thanks for pointing it out!

[jlacko]

I have amended the dev version of RCzechia package for the issues raised by @nickbearman. This included update of the journal article (adding library calls to code samples). I am thankful for the comments, as they led to improvement of the package for users.

I am not sure what the usual practice is, but I would like to add @nickbearman as [rev] in package description in a future version, as I really appreciated his view.

@editorialbot generate pdf

[martinfleis]

@editorialbot generate pdf

[jlacko]

Perfect; I will do that.

The current version is tagged as v1.10.2 / https://github.com/jlacko/RCzechia/releases/tag/v1.10.2

It is listed on Zenodo as https://zenodo.org/record/7665574

The metadata on Zenodo is the same as in the article / in particular the author is me (using the same ORCID as the JOSS article) and the title is the same as of the JOSS article.

The Zenodo tagged version has DOI 10.5281/zenodo.7665574

[martinfleis]

@editorialbot set 10.5281/zenodo.7665574 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7665574

[martinfleis]

@editorialbot set v1.10.2 as version

[editorialbot]

Done! version is now v1.10.2

[martinfleis]

Thanks @jlacko! That is all done from my side. I am going to recommend acceptance and pass the submission to the editor in chief.

Big thanks to @nickbearman and @paleolimbot for their reviews! We couldn't run JOSS without you!

[martinfleis]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Couldn't check the bibtex because branch name is incorrect: joss-paper

[editorialbot]

⚠️ Error preparing paper acceptance.

[martinfleis]

@editorialbot set master as branch

[editorialbot]

Done! branch is now master

[martinfleis]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[jlacko]

I am sorry; this is my fault - I have closed the branch; as finalized.

[editorialbot]

👋 @openjournals/sbcs-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#4008, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[editorialbot]

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

OK DOIs

- 10.1038/s41598-021-02545-z is OK
- 10.25225/jvb.21016 is OK
- 10.32614/RJ-2018-009 is OK
- 10.21105/joss.02948 is OK
- 10.5281/ZENODO.4317946 is OK
- 10.1007/s10109-020-00336-0 is OK
- 10.2307/1218258 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[martinfleis]

@jlacko no worries, that was na easy fix :)

[jlacko]

@martinfleis thanks for your understanding!

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05082 joss-papers#4011
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05082
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@nickbearman, @paleolimbot – many thanks for your reviews here and to @martinfleis for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@jlacko – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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

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[jlacko]

Thank you all for the review and opportunity to learn. The comments from @nickbearman and @paleolimbot made the package better, and I learned a lot in the process. You rock!