[REVIEW]: lpcde: Estimation and Inference for Local Polynomial Conditional Density Estimators

[editorialbot]

Submitting author: !--author-handle-->@rajitachandak<!--end-author-handle-- (Rajita Chandak) Repository: https://github.com/nppackages/lpcde Branch with paper.md (empty if default branch): Version: v.0.1.4 Editor: !--editor-->@spholmes<!--end-editor-- Reviewers: !--reviewers-list-->@salbalkus<!--end-reviewers-list-- Archive: Pending

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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

@salbalkus, 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 @spholmes 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 @salbalkus

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1412.3 files/s, 210342.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               22            436           1619           2422
Markdown                         5             54              0            156
TeX                              2             21              4            139
YAML                             3             15              6             93
C++                              2             16             22             61
-------------------------------------------------------------------------------
SUM:                            34            542           1651           2871
-------------------------------------------------------------------------------

Commit count by author:

   103  Rajita Chandak
    14  Matias D. Cattaneo

[editorialbot]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: Local Polynomial Conditional Density Estimators
- No DOI given, and none found for title: lpcde: Estimation and Inference for Local Polynomi...
- No DOI given, and none found for title: On Conditional Density Estimation
- No DOI given, and none found for title: Local Polynomial Modelling and Its Applications
- No DOI given, and none found for title: Smoothing Methods in Statistics
- No DOI given, and none found for title: Kernel Smoothing
- No DOI given, and none found for title: Nonparametric Econometrics: The np Package
- No DOI given, and none found for title: ggplot2: Elegant Graphics for Data Analysis
- No DOI given, and none found for title: Conditional Density Estimation with Neural Network...

❌ MISSING DOIs

- 10.1080/01621459.2017.1285776 may be a valid DOI for title: On the Effect of Bias Estimation on Coverage Accur...
- 10.3150/21-bej1445 may be a valid DOI for title: Coverage Error Optimal Confidence Intervals for Lo...
- 10.1093/biomet/83.1.189 may be a valid DOI for title: Estimation of Conditional Densities and Sensitivit...
- 10.1198/016214504000000548 may be a valid DOI for title: Cross-Validation and the Estimation of Conditional...
- 10.2307/2669691 may be a valid DOI for title: Methods for Estimating a Conditional Distribution ...
- 10.2307/1270280 may be a valid DOI for title: Multivariate Density Estimation: Theory, Practice,...
- 10.32614/cran.package.hdrcde may be a valid DOI for title: hdrcde: Highest Density Regions and Conditional De...

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 876

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[editorialbot]

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

[salbalkus]

Review checklist for @salbalkus

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/nppackages/lpcde?
• [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 (@rajitachandak) 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?

[salbalkus]

Hi @rajitachandak, I have a few substantive comments on the software that I'd like to post as issues in the GitHub repo, as recommended by JOSS. Would you mind enabling the "Issues" tab on your package's repo so that I can do so? Thanks!

[rajitachandak]

Hello @salbalkus, I have enabled Issues/Discussions for the repo, you should now be able to add your comments there. Thanks!

[salbalkus]

Adding issues raised as I go along:

• [x] JOSS review: Add community guidelines nppackages/lpcde#5
• [x] JOSS review: Fix license nppackages/lpcde#6
• [x] JOSS review: Software paper citations and spelling nppackages/lpcde#7
• [x] JOSS review: Unit tests nppackages/lpcde#8
• [x] JOSS review: Functionality for predicting densities nppackages/lpcde#9
• [x] JOSS review: Automatic bandwidth selection error nppackages/lpcde#10

[salbalkus]

Hi @rajitachandak my first pass is now complete; overall, the paper and the software look great. The remaining unchecked items pertain to some issues that I've filed above; @spholmes I assume I should wait to check these until the issues have been addressed? Thanks!

[rajitachandak]

Dear @salbalkus,

Thank you for your thorough review and feedback of our package and paper. We have addressed each of the issues raised on our repository and provided a note regarding the changes we have made on each issue individually. Just to summarize our revision -- We made all the changes requested. We have added a discussion on the issue regarding implementing the predict method that we hope will help explain our implementation of this request.

Please feel free to reach out if you have any questions.

[salbalkus]

Hi @rajitachandak,

Thank you for the in-depth explanations and attention to detail on this response. All of my previous concerns have been addressed! As noted in JOSS review: Fix license nppackages/lpcde#6 the only remaining issue I see is to change the GPL license GitHub shield and license tabs in the README to be consistent with the MIT license that you have included. Once that is complete, I will recommend the software for publication!

[rajitachandak]

Dear @salbalkus,

Thanks for pointing out that inconsistency! I have update all license files in our repository to GPL >=3.0. The changes will reflect on CRAN shortly.

[salbalkus]

Hi @rajitachandak,

Thanks again for the update. It looks like I'm still seeing an MIT license in the README.md file located in the top level of the repository (the one that displays at this link directly). It is located in the section titled "License", just after the "References" section that cites your papers.

Since the GPL license is included in a separate file elsewhere it may be best to just remove this section of the top level README.md.

[rajitachandak]

Dear @salbalkus,

Done, thanks!

[salbalkus]

Hi @spholmes, just wanted to let you know I've completed my review! I am recommending to accept.