[REVIEW]: bwsample: Processing Best-Worst Scaling data

[whedon]

Submitting author: @ulf1 (Ulf Hamster)
Repository: https://github.com/satzbeleg/bwsample
Version: v0.6.9
Editor: @mikldk
Reviewer: @ejhigson, @jakryd
Archive: 10.5281/zenodo.5233945

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Review checklist for @ejhigson

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

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General checks

• Repository: Is the source code for this software available at the repository url?
• 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 (@ulf1) 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 and who the target audience is?
• 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?

Review checklist for @jakryd

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 repository url?
• 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 (@ulf1) 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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ejhigson, @jakryd it looks like you're currently assigned to review this paper 🎉.

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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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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (356.0 files/s, 53864.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          20            454            836           1404
Markdown                         3             92              0            244
Jupyter Notebook                 3              0           1377            108
TeX                              1              7              0             94
YAML                             3              8              0             48
JSON                             1              0              0             18
-------------------------------------------------------------------------------
SUM:                            31            561           2213           1916
-------------------------------------------------------------------------------


Statistical information for the repository 'e6dd3d2358dd55d2afd32d0b' was
gathered on 2021/06/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
UH                              68          3654            960          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
UH                         2694           73.7          1.7                7.72

[whedon]

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

OK DOIs

- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1177/074391569201100202 is OK
- 10.1016/S0377-2217(02)00227-8 is OK
- 10.1214/aos/1079120141 is OK
- 10.31219/osf.io/qkxej is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[mikldk]

@ejhigson, @jakryd: Thanks for agreeing to review. Please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

[whedon]

👋 @ejhigson, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @jakryd, please update us on how your review is going (this is an automated reminder).

[ejhigson]

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mikldk know.

Hi @mikldk - I'm trying to update my checklist but I can't edit it. When I click on https://github.com/openjournals/joss-reviews/invitations I get a message saying "Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account." Do you know what has gone wrong here? Please could you perhaps resend my invitation to do the review? Thank you!

[mikldk]

@whedon re-invite @ejhigson as reviewer

[whedon]

OK, the reviewer has been re-invited.

@ejhigson please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[ejhigson]

@whedon re-invite @ejhigson as reviewer

This has worked, thank you @mikldk!

[mikldk]

@jakryd, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

[jakryd]

Sorry for the delay, @mikldk. I'm almost over with my review.

@ulf1 -- Have you compared how your methods perform in comparison to other commonly-used packages?

[ulf1]

Sorry for the delay, @mikldk. I'm almost over with my review.

@ulf1 -- Have you compared how your methods perform in comparison to other commonly-used packages?

To my surprise, I haven't found a package that suited our needs. There exists a commercial software vendor (Sawtooth Software) who offers Best-Worst-Scaling surveys since the 80s/90s. It looks that they are related to the research community about BWS in the 90s.
Our UI (see page 2 in https://osf.io/qkxej/) and Sawtooth's UI (see https://sawtoothsoftware.com/maxdiff) will produce the same kind of data but that's basically all. The 80s/90s BWS method is classic statistics, e.g. items will be shown several times over and over again. The assumptions is that the number of items is somewhat limited.
In our use case we have billions of items to assess (sentence examples) but still the same human resource limitations. As a result we had the idea to transform the BWS data in paired comparison data, and logical infer even more pairs (see Ch.4 in https://osf.io/qkxej/). This was implemented in bwsample.count. This approach requires also a certain kind of sampling strategy (see Ch.5 in https://osf.io/qkxej/) what is available in bwsample.sample.
Regarding the ranking of the (big) sparse matrix with paired comparisons (database with up to billions^2 pairs), i prefer the most simple approaches (e.g. bwsample.rank(..., "ratio")) because the update can be done with linear complexity in production. The package also includes more theoretical sound approaches (e.g. BTL Maximum Likelihood). The little experiment in Ch.7 (https://osf.io/ev7fw/) shows that the BTL models basically produce the same rankings. However, the problem is that approaches like BTL-model, Eigenvector, etc. require a complete re-computation that is O(n^2) complex what is infeasible in our production scenario.

[jakryd]

I see. As you provided https://doi.org/10.31219/osf.io/qkxej in the references, I think that anyone interested in this issue can find more information there.

No further questions from me. I'm happy to recommend this paper for publication.

[mikldk]

@ejhigson can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

@jakryd: Can you please check the last box if you think this item is also okay?

[ejhigson]

Apologies for the delay - I plan to do this in the next couple of weeks!

[mikldk]

@jakryd - thanks for completing the checklist.

@ejhigson - thanks for the update 👍.

[ejhigson]

Hi @ulf1 - congratulations on a nice software package! Everything ran with no issues for me. I only have a couple of very minor comments on the paper:

1. One of the criteria is to state "how this software compares to other commonly-used packages" - please can you comment on this? If you don't know of any other best-worst sampling packages then just stating that is fine I think.

2. I saw a few small typos:
   L16 “software feature” -> “software features”
   L19 “items has to be shown” -> “items have to be shown”
   L20 “reasonable amounts counting” -> “reasonable amounts of counting

[ulf1]

@ejhigson

1. No, I don't know comparable software packages. See also the comment above [REVIEW]: bwsample: Processing Best-Worst Scaling data #3324 (comment)
2. Thank you for spotting the typos.

[ejhigson]

@ejhigson

1. No, I don't know comparable software packages. See also the comment above [REVIEW]: bwsample: Processing Best-Worst Scaling data #3324 (comment)
2. Thank you for spotting the typos.

Thank you very much for this, and sorry I had missed the above comment! I have now completed my review.

[mikldk]

@ejhigson, @jakryd: Can you confirm that you have finished the review and recommend that this paper is now published once ulf1/bwsample#72 is closed?

@ulf1 Please ping me once ulf1/bwsample#72 is closed and that you had a final read though of the paper, checking language etc. and a final check of the proofs with @whedon generate pdf.

[jakryd]

I have completed my review and recommend the paper for publication.

[whedon]

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

[mikldk]

@ulf1 Title and authors still not consistent across paper and archive. Please fix and ping me once completed.

[ulf1]

@mikldk the title and author name are aligned now.

• https://doi.org/10.5281/zenodo.5233945
• https://github.com/satzbeleg/bwsample/blob/main/.zenodo.json
• https://github.com/satzbeleg/bwsample/blob/main/docs/paper.md

[mikldk]

@whedon set 10.5281/zenodo.5233945 as archive

[whedon]

OK. 10.5281/zenodo.5233945 is the archive.

[mikldk]

@whedon check references

[whedon]

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

OK DOIs

- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1177/074391569201100202 is OK
- 10.1016/S0377-2217(02)00227-8 is OK
- 10.1214/aos/1079120141 is OK
- 10.31219/osf.io/qkxej is OK

MISSING DOIs

- None

INVALID DOIs

- None

[mikldk]

@whedon generate pdf

[whedon]

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

[mikldk]

@whedon set v0.6.9 as version

[whedon]

OK. v0.6.9 is the version.

[mikldk]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1177/074391569201100202 is OK
- 10.1016/S0377-2217(02)00227-8 is OK
- 10.1214/aos/1079120141 is OK
- 10.31219/osf.io/qkxej is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2521

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2521, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

👋 @ulf1 - As the AEiC on duty this week, I've suggested some changes to the paper in ulf1/bwsample#75 - please merge this, or let me know what you disagree with. Once we do this, we can proceed to final publication.

[ulf1]

@danielskatz Thank you, I merged your corrections.

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03324 joss-papers#2524
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03324
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...

[danielskatz]

Congratulations to @ulf1 (Ulf Hamster)!!

And thanks to @mikldk for editing, and to @ejhigson and @jakryd for reviewing!

[whedon]

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

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