[REVIEW]: PyEI: A Python package for ecological inference

[whedon]

Submitting author: @karink520 (Karin Knudson)
Repository: https://github.com/mggg/ecological-inference
Version: v0.1.1
Editor: @drvinceknight
Reviewer: @matt-graham, @pmyteh
Archive: 10.5281/zenodo.5245632

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Status

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Markdown: [![status](https://joss.theoj.org/papers/6915a867f5b1185488f1d4a8e856e2f3/status.svg)](https://joss.theoj.org/papers/6915a867f5b1185488f1d4a8e856e2f3)

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Review checklist for @matt-graham

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 (@karink520) 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 @pmyteh

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 (@karink520) 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. @matt-graham, @pmyteh 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.

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@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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.07 s (348.7 files/s, 255310.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          12            459            945           1975
Jupyter Notebook                 6              0          14086            451
TeX                              1             19              0            137
Markdown                         2             53              0            116
YAML                             1              4              2             25
Bourne Shell                     3             11              0             21
-------------------------------------------------------------------------------
SUM:                            25            546          15033           2725
-------------------------------------------------------------------------------


Statistical information for the repository '95325e035168347ecb2bdc86' was
gathered on 2021/06/23.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Amy Becker                       2            49             17            0.88
Colin Carroll                   13           358            252            8.12
Gabe Schoenbach                 30           693            269           12.81
JN                               1            17             10            0.36
Karin Knudson                   96          3957           1369           70.94
Matthew Sun                     16           357            149            6.74
karink520                        6             7              4            0.15

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
Amy Becker                   28           57.1          1.6                3.57
Colin Carroll               200           55.9          3.8                9.00
Gabe Schoenbach             505           72.9          1.7                3.96
JN                           11           64.7          0.3                0.00
Karin Knudson              2405           60.8          4.5                8.32
Matthew Sun                 230           64.4          8.7                9.13

[whedon]

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

OK DOIs

- 10.2307/2088121 is OK
- 10.21105/joss.01143 is OK
- 10.1093/acprof:oso/9780198515326.001.0001 is OK
- 10.1201/b10905-7 is OK

MISSING DOIs

- 10.3886/icpsr01132.v1 may be a valid DOI for title: A solution to the ecological inference problem: Reconstructing individual behavior from aggregate data

INVALID DOIs

- None

[whedon]

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

[whedon]

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

[whedon]

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

[drvinceknight]

Could you make a tagged release and archive, and report the version number and archive DOI here please.

Please make sure the archive has the correct metadata: ie that the title and author list match the paper.

[karink520]

@drvinceknight Done! Version number: v0.1.1. DOI: DOI: 10.5281/zenodo.5245632

[drvinceknight]

@whedon set 10.5281/zenodo.5245632 as archive

[whedon]

OK. 10.5281/zenodo.5245632 is the archive.

[drvinceknight]

@whedon set v0.1.1 as version

[whedon]

OK. v0.1.1 is the version.

[drvinceknight]

@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

- 10.2307/2088121 is OK
- 10.1111/j.1467-985X.2008.00551.x is OK
- 10.1515/9781400849208 is OK
- 10.1177/0049124199028001004 is OK
- 10.1111/j.1467-985x.2004.02046.x is OK
- 10.1111/1467-9574.00162 is OK
- 10.21105/joss.01143 is OK
- 10.7717/peerj-cs.55 is OK
- 10.1093/acprof:oso/9780198515326.001.0001 is OK
- 10.1201/b16018 is OK
- 10.1201/b10905-7 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#2533

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2533, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[karink520]

Wonderful! Thanks again, all!

[karink520]

Er, excuse my confusion, but am I the one who should run that last compile with deposit=true ? Or that instruction is aimed at someone else?

[danielskatz]

No, I will do that as the AEiC on duty this week after I proofread the paper and check a few others things.

[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.03397 joss-papers#2535
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03397
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 @karink520 (Karin Knudson) and co-authors!!

And thanks to @drvinceknight for editing, and @matt-graham and @pmyteh for reviewing!
We couldn't do this without you!

[whedon]

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

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