[REVIEW]: samplics: a Python Package for selecting, weighting and analyzing data from complex sampling designs.

[whedon]

Submitting author: @MamadouSDiallo (Mamadou Diallo)
Repository: https://github.com/survey-methods/samplics/
Version: 0.2.6
Editor: @arfon
Reviewer: @rchew, @soodoku
Archive: 10.5281/zenodo.5750761

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/2289ce48fba67b7260b08178adb50ebf/status.svg)](https://joss.theoj.org/papers/2289ce48fba67b7260b08178adb50ebf)

Reviewers and authors:

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

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✨ 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 ✨

Review checklist for @rchew

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 (@MamadouSDiallo) 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? #3801
• 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 @soodoku

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 (@MamadouSDiallo) 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. @rchew, @soodoku it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1007/0-387-31075-4_3 may be a valid DOI for title: Sampling With Unequal Probabilities
- 10.1111/1468-0262.00399 may be a valid DOI for title: Micro-level estimation of poverty and inequality

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.51 s (355.8 files/s, 186236.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            34           2106             34          23486
CSS                             42           1221            398          14515
JavaScript                      17           3562           3039          12330
Python                          55           2865           1632          11654
Jupyter Notebook                12              0          15651            927
SVG                              1              0              0            288
Markdown                         2             64              0            190
reStructuredText                11            127            158            144
TeX                              1             11              0             81
TOML                             1             11              6             74
YAML                             2              5              6             68
INI                              1              5              0             27
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           181           9989          20932          63819
-------------------------------------------------------------------------------


Statistical information for the repository '883530d9ce3e8dca45563791' was
gathered on 2021/06/16.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Mamadou S Diallo               593        427901         371816          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
Mamadou S Diallo          35082            8.2          4.3               10.81

[whedon]

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

[arfon]

@rchew, @soodoku – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. 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.

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 pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/3376 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[soodoku]

For stats packages, I am going to sign off on 'functionality' without checking for correctness as that will take a sig. investment. I have proposed a way to match outputs to other implementations like Lumley's R version. But I am assuming the bar for acceptance is lower.

[whedon]

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

[whedon]

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

[arfon]

👋 @rchew – how are you getting along here with your review?

[arfon]

@whedon re-invite @rchew as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[arfon]

@MamadouSDiallo – I'm sorry this submission is taking so long, I've just emailed @rchew to see if they can complete their review in the next couple of weeks. If not, I think we'll need to find an alternative second reviewer.

[MamadouSDiallo]

@arfon thank you very much for the update. I am looking forward to the second review. Best regards

[rchew]

@arfon Apologies for the delay, would you be willing to resend an invite?

[arfon]

@whedon re-invite @rchew as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[arfon]

@arfon Apologies for the delay, would you be willing to resend an invite?

@rchew – please try again now?

[rchew]

@arfon Received new invitation -- thanks!

[rchew]

@MamadouSDiallo Apologies once again for how long this has taken to review. Started adding some issues to your repo and wanted to tag in this thread as well.

Started with following the examples on the README using the version on pip, but it appears that the pip version is out of date with the documentation and the code on GH. Will clone the repo locally for the time being to address the other components of the library.

• Documentation outdated in README and ReadTheDocs samplics-org/samplics#34

[rchew]

@MamadouSDiallo Finished an initial review, and overall, this looks like it's in pretty good shape! Still assessing Functionality and Documentation, but wanted to bring your attention to @soodoku 's comments if you hadn't yet seen them:

• fix use of some deprecated things samplics-org/samplics#29
• testing samplics-org/samplics#30
• comm. guidelines samplics-org/samplics#31
• minor issues w/ writing samplics-org/samplics#32

[arfon]

@MamadouSDiallo – looks like there's a bunch of great feedback from @soodoku and @rchew here. Please let us know when you might be able to address this feedback.

[MamadouSDiallo]

@arfon thank you for the reminder. I will work on these issues during the weekend and come back to you early next week. Also, thanks to @rchew and @soodoku for the review.

[arfon]

@whedon assign me as editor

Unfortunately @lorenanicole is no longer able to edit this submission so I'll be taking over from here.

[MamadouSDiallo]

Sorry for the delay
10.5281/zenodo.5750761

[arfon]

@whedon set 10.5281/zenodo.5750761 as archive

[whedon]

OK. 10.5281/zenodo.5750761 is the archive.

[arfon]

@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

- 10.1007/978-1-4684-9407-5 is OK
- 10.1111/1468-0262.00399 is OK
- 10.18637/jss.v009.i08 is OK
- 10.1002/cjs.10051 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#2794

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2794, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@MamadouSDiallo – is there any way you can tweak the layout of your equations to stop the text falling into the margins...

[MamadouSDiallo]

Somehow the editor was witching _ to *
I hope it's fixed now. Let me know.

[arfon]

@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

- 10.1007/978-1-4684-9407-5 is OK
- 10.1111/1468-0262.00399 is OK
- 10.18637/jss.v009.i08 is OK
- 10.1002/cjs.10051 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#2798

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2798, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@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.03376 joss-papers#2800
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03376
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]

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

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

[whedon]

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

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.03376/status.svg)](https://doi.org/10.21105/joss.03376)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03376/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03376/status.svg
   :target: https://doi.org/10.21105/joss.03376

This is how it will look in your documentation:

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[MamadouSDiallo]

Dear @whedon, @arfon, @rchew , @soodoku

Thank you very much for the review. It was really a pleasure working with you.

Best wishes to you all

[MamadouSDiallo]

Dear @whedon

I found a typo in the paper I don't know if it's still possible to fix.
The typo is "let us us us" in Sample Estimation section.

I fixed it in my github copy.

Best regards

[danielskatz]

👋 @arfon

I found a typo in the paper I don't know if it's still possible to fix.
The typo is "let us us us" in Sample Estimation section.

I fixed it in my github copy.

[arfon]

@MamadouSDiallo – I just fixed this in the JOSS copy too. It may take 24 hours for the new version to show up on the JOSS website due to caching.