[REVIEW]: densify: An R package to prune sparse data frames of typological linguistic data

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@annagraff@osorensen<!--end-editor-- Reviewers: @elenlefoll, @yjunechoe, @stefanocoretta Archive: 10.5281/zenodo.13384828

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/e896a6a49ef4fd23d6b2c0c835f9954e/status.svg)](https://joss.theoj.org/papers/e896a6a49ef4fd23d6b2c0c835f9954e)

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

@elenlefoll, 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 @osorensen 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 @elenlefoll

📝 Checklist for @yjunechoe

📝 Checklist for @stefanocoretta

editorialbot commented 3 months ago

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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 3 months ago

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

OK DOIs

- 10.5281/zenodo.7385533 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.5281/zenodo.7976754 is OK
- 10.5281/zenodo.7836668 is OK
- 10.5281/zenodo.2677911 is OK
- 10.5281/zenodo.7740140 is OK
- 10.5281/zenodo.10804357 is OK

MISSING DOIs

- 10.32614/cran.package.admmdensestsubmatrix may be a valid DOI for title: admmDensestSubmatrix: Alternating Direction Method...
- 10.32614/cran.package.fselector may be a valid DOI for title: FSelector: Selecting Attributes
- 10.32614/cran.package.varrank may be a valid DOI for title: varrank: Heuristics Tools Based on Mutual Informat...

INVALID DOIs

- None

editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1537.0 files/s, 197948.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               19            374            444           1104
Rmd                              1            161            540            439
Markdown                         4             54              0            177
CSV                              1              0              0            162
TeX                              2             10              0            119
YAML                             1              0              4             18
-------------------------------------------------------------------------------
SUM:                            28            599            988           2019
-------------------------------------------------------------------------------

Commit count by author:

   121  Anna Graff
    77  Marc Lischka
    21  marclischka
    11  Taras Zakharko
     9  Work
     5  reinhardfurrer
     2  Balthasar Bickel

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 1319

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

🟡 License found: GNU Affero General Public License v3.0 (Check here for OSI approval)

osorensen commented 3 months ago

@elenlefoll this is the review issue. Please let me know if you have any questions.

I will keep looking for one or more additional reviewers.

editorialbot commented 3 months ago

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

osorensen commented 3 months ago

:wave: @yjunechoe @stefanocoretta @dosc91 would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

elenlefoll commented 3 months ago

Review checklist for @elenlefoll

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/annagraff/densify?
[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 (@annagraff) 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?

yjunechoe commented 3 months ago

@osorensen Happy to review!

osorensen commented 3 months ago

Wonderful @yjunechoe!

osorensen commented 3 months ago

@editorialbot add @yjunechoe as reviewer

editorialbot commented 3 months ago

@yjunechoe added to the reviewers list!

osorensen commented 3 months ago

@yjunechoe, I have added you as a reviewer, and you are welcome to start your review whenever you like, but it would be great if you could do so within the next three weeks. You find instructions at the top of this thread, and are welcome to reach out to me if you have any questions.

stefanocoretta commented 3 months ago

Hi @osorensen ! Happy to review too if you need a second

osorensen commented 3 months ago

@editorialbot add @stefanocoretta as reviewer

editorialbot commented 3 months ago

@stefanocoretta added to the reviewers list!

osorensen commented 3 months ago

Thanks @stefanocoretta. You see the instructions at the top of this thread. Please reach out to me if you have any questions.

yjunechoe commented 3 months ago

Review checklist for @yjunechoe

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/annagraff/densify?
[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 (@annagraff) 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?

yjunechoe commented 3 months ago

Just curious - @annagraff do you/coauthors have plans to eventually submit the package to CRAN as well? I have some suggestions which are beyond the standards of JOSS (i.e., not acceptance-blocking) but may be helpful to get the package past the initial submission check by CRAN.

annagraff commented 3 months ago

Hello @yjunechoe - this would be our intention, yes!

yjunechoe commented 3 months ago

@osorensen I raised this as a checklist comment for the software paper but I now feel a bit uncertain - could you clarify whether demonstrating package design/features via code blocks is allowed for JOSS papers? In the review criteria, I see:

Note the paper should not include software documentation such as API (Application Programming Interface) functionality, as this should be outlined in the software documentation.

The paper in this submission contains example code, but is not quite documentation of the API, so I'm having trouble evaluating the current case.

osorensen commented 3 months ago

@osorensen I raised this as a checklist comment for the software paper but I now feel a bit uncertain - could you clarify whether demonstrating package design/features via code blocks is allowed for JOSS papers? In the review criteria, I see:

Note the paper should not include software documentation such as API (Application Programming Interface) functionality, as this should be outlined in the software documentation.

The paper in this submission contains example code, but is not quite documentation of the API, so I'm having trouble evaluating the current case.

Thanks for raising the issue @yjunechoe. Looking at the paper, I feel this is more detailed code than usual JOSS paper. I hence agree with you that this belongs in README and/or vignettes, and that the paper instead should focus on the high-level architecture of the software.

elenlefoll commented 2 months ago

@elenlefoll this is the review issue. Please let me know if you have any questions.

I will keep looking for one or more additional reviewers.

I have completed the review check list. Is there anything else that I need to do?

osorensen commented 2 months ago

Thanks for your review, @elenlefoll. There is nothing more you need to do know. We appreciate your work.

osorensen commented 2 months ago

@stefanocoretta can you please update us on how it's going with your review?

stefanocoretta commented 2 months ago

Review checklist for @stefanocoretta

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/annagraff/densify?
[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 (@annagraff) 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?

stefanocoretta commented 2 months ago

@stefanocoretta can you please update us on how it's going with your review?

Very sorry for the delay! It was very busy at work with dissertations.

annagraff commented 2 months ago

Hi @stefanocoretta, do I understand correctly that your review is already complete with no new issues? If this is the case, I will proceed to soon push the changes made to address issues raised by @elenlefoll and @yjunechoe.

yjunechoe commented 2 months ago

Just to expedite the process: I've read through the revisions in the draft PR and I'm really happy with all the changes I see, so I've checked off all boxes for my review. I think the submission can move forward to the next step.

One small follow-up suggestion to authors: it'd be nice if the README could also print the output of some of the code being ran (vs. having every line be an assignment to a variable).

osorensen commented 2 months ago

@annagraff, it seems like all reviews are completed then. I'll read through the paper soon, and let you know if I have any further comments.

osorensen commented 2 months ago

@editorialbot generate pdf

osorensen commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

editorialbot commented 2 months ago

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

✅ OK DOIs

- 10.5281/zenodo.7385533 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.5281/zenodo.7976754 is OK
- 10.5281/zenodo.7836668 is OK
- 10.5281/zenodo.2677911 is OK
- 10.5281/zenodo.7740140 is OK
- 10.5281/zenodo.10804357 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- 10.32614/cran.package.admmdensestsubmatrix may be a valid DOI for title: admmDensestSubmatrix: Alternating Direction Method...
- 10.32614/cran.package.fselector may be a valid DOI for title: FSelector: Selecting Attributes
- 10.32614/cran.package.varrank may be a valid DOI for title: varrank: Heuristics Tools Based on Mutual Informat...

❌ INVALID DOIs

- None

annagraff commented 2 months ago

@osorensen: I still need to merge the changes to the paper to main, which I will do once Stefano confirms there are are no further issues from his end

osorensen commented 2 months ago

@annagraff, you don't really have to wait for that, since completing the checklist implies that the review is completed, as far as JOSS is concerned.

osorensen commented 2 months ago

@annagraff, any progress on merging the changes into main?

annagraff commented 2 months ago

Sorry for the delay, I have just merged them now!

On 26 Aug 2024, at 21:24, Øystein Sørensen @.***> wrote:

@annagraff https://github.com/annagraff, any progress on merging the changes into main?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7024#issuecomment-2310913959, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKEXNOPM5YBITBXWBLDCLF3ZTN6IBAVCNFSM6AAAAABLKHMGZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJQHEYTGOJVHE. You are receiving this because you were mentioned.

osorensen commented 2 months ago

@editorialbot generate pdf

osorensen commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

✅ OK DOIs

- 10.5281/zenodo.7385533 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.5281/zenodo.7976754 is OK
- 10.5281/zenodo.7836668 is OK
- 10.5281/zenodo.2677911 is OK
- 10.5281/zenodo.7740140 is OK
- 10.5281/zenodo.10804357 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- 10.32614/cran.package.admmdensestsubmatrix may be a valid DOI for title: admmDensestSubmatrix: Alternating Direction Method...
- 10.32614/cran.package.fselector may be a valid DOI for title: FSelector: Selecting Attributes
- 10.32614/cran.package.varrank may be a valid DOI for title: varrank: Heuristics Tools Based on Mutual Informat...

❌ INVALID DOIs

- None

editorialbot commented 2 months ago

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

osorensen commented 2 months ago

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

✅ OK DOIs

- 10.5281/zenodo.7385533 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.5281/zenodo.7976754 is OK
- 10.5281/zenodo.7836668 is OK
- 10.5281/zenodo.2677911 is OK
- 10.5281/zenodo.7740140 is OK
- 10.5281/zenodo.10804357 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- 10.32614/cran.package.admmdensestsubmatrix may be a valid DOI for title: admmDensestSubmatrix: Alternating Direction Method...
- 10.32614/cran.package.fselector may be a valid DOI for title: FSelector: Selecting Attributes
- 10.32614/cran.package.varrank may be a valid DOI for title: varrank: Heuristics Tools Based on Mutual Informat...

❌ INVALID DOIs

- None

@annagraff, I've now read through the paper, and everything looks good. However, could you please add the suggested DOIs to the R packages that you are citing, and then let me know when this is done?

annagraff commented 2 months ago

Hi @osorensen https://github.com/osorensen, I have added the DOIs. Thank you very much!

On 28 Aug 2024, at 13:52, Øystein Sørensen @.***> wrote:

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

✅ OK DOIs

10.5281/zenodo.7385533 is OK

10.1093/bioinformatics/bty633 is OK

10.5281/zenodo.7976754 is OK

10.5281/zenodo.7836668 is OK

10.5281/zenodo.2677911 is OK

10.5281/zenodo.7740140 is OK

10.5281/zenodo.10804357 is OK

🟡 SKIP DOIs

None

❌ MISSING DOIs

10.32614/cran.package.admmdensestsubmatrix may be a valid DOI for title: admmDensestSubmatrix: Alternating Direction Method...

10.32614/cran.package.fselector may be a valid DOI for title: FSelector: Selecting Attributes

10.32614/cran.package.varrank may be a valid DOI for title: varrank: Heuristics Tools Based on Mutual Informat...

❌ INVALID DOIs

None @annagraff https://github.com/annagraff, I've now read through the paper, and everything looks good. However, could you please add the suggested DOIs to the R packages that you are citing, and then let me know when this is done?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7024#issuecomment-2315118252, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKEXNOPBHX6NXBFVPI7YIXDZTW2ZNAVCNFSM6AAAAABLKHMGZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJVGEYTQMRVGI. You are receiving this because you were mentioned.

osorensen commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

✅ OK DOIs

- 10.5281/zenodo.7385533 is OK
- 10.32614/cran.package.admmdensestsubmatrix is OK
- 10.32614/cran.package.fselector is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.5281/zenodo.7976754 is OK
- 10.5281/zenodo.7836668 is OK
- 10.5281/zenodo.2677911 is OK
- 10.5281/zenodo.7740140 is OK
- 10.5281/zenodo.10804357 is OK
- 10.32614/cran.package.varrank is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

osorensen commented 2 months ago

@annagraff, 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 recommending acceptance.

annagraff commented 2 months ago

@osorensen https://github.com/osorensen:

The version tag is 1.0.0.
The DOI of the archival deposit on Zenodo is the following: 10.5281/zenodo.13384828

On 28 Aug 2024, at 16:04, Øystein Sørensen @.***> wrote:

@annagraff https://github.com/annagraff, 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 recommending acceptance.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7024#issuecomment-2315414033, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKEXNOMOR3XUWGVOCDD6A7DZTXKFTAVCNFSM6AAAAABLKHMGZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJVGQYTIMBTGM. You are receiving this because you were mentioned.

osorensen commented 2 months ago

@editorialbot set 1.0.0 as version

openjournals / joss-reviews