[REVIEW]: sptotal: an R package for predicting totals and weighted sums from spatial data

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@highamm@fabian-s<!--end-editor-- Reviewers: @Athene-ai, @garretrc Archive: 10.5281/zenodo.7962631

Status

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Markdown: [![status](https://joss.theoj.org/papers/30a8945e4138d482c484e4f9b7ce2b7a/status.svg)](https://joss.theoj.org/papers/30a8945e4138d482c484e4f9b7ce2b7a)

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

@Athene-ai & @garretrc, 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 @fabian-s 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 @Athene-ai

📝 Checklist for @garretrc

editorialbot commented 1 year 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:

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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 commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (1453.8 files/s, 201078.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            46           1450            180           6282
R                               29            417           1118           1194
XML                              3              0              2            606
Markdown                         5            158              0            495
CSS                              3             98             52            442
JavaScript                       4             64             34            266
Rmd                              2            176            325            166
YAML                             6             27             12            139
TeX                              1             10              0            106
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           100           2400           1724           9707
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1242

editorialbot commented 1 year ago

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

OK DOIs

- 10.1371/journal.pone.0282524 is OK
- 10.32614/rj-2018-009 is OK
- 10.1080/11956860.2002.11682701 is OK
- 10.1111/2041-210X.13919 is OK
- 10.1371/journal.pone.0059129 is OK
- 10.1037/e471672008-001 is OK
- 10.1007/s10651-007-0035-y is OK
- 10.1016/j.cageo.2004.03.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

fabian-s commented 1 year ago

Hi @Athene-ai & @garretrc, thanks again for agreeing to review this. Please read the top level comment in this thread and create your reviewer checklists.

fabian-s commented 1 year ago

Athene-ai commented 1 year ago

Review checklist for @Athene-ai

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/highamm/sptotal?
[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 (@highamm) 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?

garretrc commented 1 year ago

Review checklist for @garretrc

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/highamm/sptotal?
[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 (@highamm) 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?

fabian-s commented 1 year ago

@garretrc: could you please fill the remainder of the checklist and add comments or open issues for the remaining open points in your checklist so we can discuss what steps @highamm needs to take to get this paper published?

garretrc commented 1 year ago

H

@garretrc: could you please fill the remainder of the checklist and add comments or open issues for the remaining open points in your checklist so we can discuss what steps @highamm needs to take to get this paper published?

Yes, I'll get to work this week, unfortunately up against a submission deadline today. From what I've read and messed with, I think I will have some helpful feedback!

garretrc commented 1 year ago

Still need to test out the package a bit but left a couple quick comments on the paper as an issue! Looking great so far.

fabian-s commented 1 year ago

hi @garretrc -- could you please fill the remainder of the checklist and/or update us on any problems you have identified?

garretrc commented 1 year ago

Done! Ran some tests for installation + functionality on ubuntu and mac, everything looks great and the results are as expected.

fabian-s commented 1 year ago

@editorialbot generate pdf

fabian-s commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1371/journal.pone.0282524 is OK
- 10.32614/rj-2018-009 is OK
- 10.1080/11956860.2002.11682701 is OK
- 10.1111/2041-210X.13919 is OK
- 10.1371/journal.pone.0059129 is OK
- 10.1037/e471672008-001 is OK
- 10.1007/s10651-007-0035-y is OK
- 10.1016/j.cageo.2004.03.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

fabian-s commented 1 year ago

@highamm -- we are ready to recommend acceptance of this paper now.

At this point could you:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] 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.
[x] List the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

highamm commented 1 year ago

@fabian-s Great, thank you for the update!

The tagged release version of the software is v1.0.1 given at https://github.com/highamm/sptotal/tree/v1.0.1

The software is now archived in Zenodo with DOI 10.5281/zenodo.7962631 at https://doi.org/10.5281/zenodo.7962631. The authors and title do match the authors and title in the paper and on the software.

The DOI for the archived version is 10.5281/zenodo.7962631

Let me know if I missed anything here!

highamm commented 1 year ago

I also want to thank @Athene-ai and @garretrc for your taking time out of your schedules to review the software, and, to thank @fabian-s for organizing the review. I (along with the package co-authors) very much appreciate it!

fabian-s commented 1 year ago

@editorialbot set 10.5281/zenodo.7962631 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.7962631

fabian-s commented 1 year ago

@editorialbot set v1.0.1 as version

editorialbot commented 1 year ago

Done! version is now v1.0.1

fabian-s commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1371/journal.pone.0282524 is OK
- 10.32614/rj-2018-009 is OK
- 10.1080/11956860.2002.11682701 is OK
- 10.1111/2041-210X.13919 is OK
- 10.1371/journal.pone.0059129 is OK
- 10.1037/e471672008-001 is OK
- 10.1007/s10651-007-0035-y is OK
- 10.1016/j.cageo.2004.03.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/ese-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/4260, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kthyng commented 1 year ago

A few items to wrap up:

[x] Check that version was updated
[x] Check that software archive exists, has been input to JOSS, and title and author list look good
[x] Check paper

kthyng commented 1 year ago

Looks good!

kthyng commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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: Higham given-names: Matt - family-names: Hoef given-names: Jay Ver - family-names: Frank given-names: Bryce - family-names: Dumelle given-names: Michael orcid: "https://orcid.org/0000-0002-3393-5529" doi: 10.5281/zenodo.7962631 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Higham given-names: Matt - family-names: Hoef given-names: Jay Ver - family-names: Frank given-names: Bryce - family-names: Dumelle given-names: Michael orcid: "https://orcid.org/0000-0002-3393-5529" date-published: 2023-05-24 doi: 10.21105/joss.05363 issn: 2475-9066 issue: 85 journal: Journal of Open Source Software publisher: name: Open Journals start: 5363 title: "sptotal: an R package for predicting totals and weighted sums from spatial data" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05363" volume: 8 title: "sptotal: an R package for predicting totals and weighted sums from spatial data" ```

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.

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year 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/4264
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05363
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng commented 1 year ago

Congrats on your new paper @highamm! Many thanks to editor @fabian-s and reviewers @Athene-ai @garretrc for your time, hard work, and expertise!!

(I'll close this issue once the DOI resolves.)

editorialbot commented 1 year ago

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

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.05363/status.svg)](https://doi.org/10.21105/joss.05363)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05363">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05363/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05363/status.svg
   :target: https://doi.org/10.21105/joss.05363

This is how it will look in your documentation:

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kthyng commented 1 year ago

@highamm if you're up for it, I'd recommend you sign up to be a reviewer! The new reviewer system is here: https://reviewers.joss.theoj.org/

highamm commented 1 year ago

@kthyng I just registered! Thank you for your help in organizing this review and thanks again to @fabian-s, @Athene-ai , and @garretrc for your time with this as well!

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