[REVIEW]: StatAid: a R package with a graphical user interface for data analysis

[whedon]

Submitting author: @VincentAlcazer (Vincent Alcazer)
Repository: https://github.com/VincentAlcazer/StatAid
Version: v1.1.2
Editor: @mikldk
Reviewer: @nistara, @adithirgis
Archive: 10.5281/zenodo.4152933

⚠️ JOSS reduced service mode ⚠️

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Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ae17f4e76e8559c635d41dfe9405da73"><img src="https://joss.theoj.org/papers/ae17f4e76e8559c635d41dfe9405da73/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ae17f4e76e8559c635d41dfe9405da73/status.svg)](https://joss.theoj.org/papers/ae17f4e76e8559c635d41dfe9405da73)

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

@nistara & @adithirgis, 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.

✨ 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 @nistara

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 (@VincentAlcazer) 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: Do the authors clearly state 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 @adithirgis

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 (@VincentAlcazer) 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: Do the authors clearly state 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. @nistara, @adithirgis 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

[mikldk]

@nistara, @adithirgis: 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]

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

OK DOIs

- 10.18637/jss.v014.i09 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[adithirgis]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[adithirgis]

Started review here.

[nistara]

@whedon check references

[whedon]

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

OK DOIs

- 10.18637/jss.v014.i09 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[nistara]

Review process started here.

[mikldk]

@VincentAlcazer, can you give a brief status on the review issues raised in the separate threads by @nistara and @adithirgis?

[VincentAlcazer]

Dear @mikldk,
I am currently working on the issues raised by the reviewers and their comments are really helping me improving the software.
Due to the pandemic evolution in France, I am also quite busy at the hospital with only few moments to work on StatAid. However, I already corrected the main issues reported and I hope I'll be able to provide my complete answer soon.
I am very sorry for this delay and will do my best to proceed through the reviewing in time.
Best regards,

[mikldk]

@VincentAlcazer No need to be sorry - take your time. I just wanted to check in, also for the reviewers' sake. Be safe.

[nistara]

Hi @VincentAlcazer, please take your time, we're in no hurry. Thanks for your important work right now during the pandemic.

[adithirgis]

Hi @VincentAlcazer, I totally agree with @nistara and @mikldk, please take your time. And please stay safe.
Take care.

[nistara]

@whedon generate pdf

[whedon]

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

[adithirgis]

Dear @mikldk,

I have completed my review process. Thanks again for inviting me to review.

Thanks @VincentAlcazer for the wonderful application. This is a really interesting and useful software!

Regards and Stay Safe
Adithi

[nistara]

@whedon generate pdf

[whedon]

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

[nistara]

Dear @mikldk and @VincentAlcazer ,

I'm done with my review. Thank you for inviting me as a reviewer. This package is pretty awesome and should help many people explore various descriptive and statistical tools and visualizations with one tool!! I also appreciate the careful consideration give to what potential users might need to customize their analysis and plots.

Best wishes,
Nistara

[VincentAlcazer]

Dear @mikldk ,

Thank you for giving me the opportunity to have my software reviewed by JOSS. I would like to thanks @nistara and @adithirgis who did an amazing job thoroughly reviewing StatAid and really helped me to improve the software.

Please let me know if there is anything else I should do now for the following submission process.

Best regards,

Vincent Alcazer

[mikldk]

@VincentAlcazer It looks like you have folders such as .Rproj.user in your Git. Please remove it by creating a .gitignore file. Check other folders, too - I am not sure about e.g. rsconnect.

[VincentAlcazer]

@mikldk it is strange as the .gitignore file already included .Rproj.user. I manually deleted the folders and added rsconnect exclusion in the .gitignore file. It seems to work correctly now.

I had to push a new version to update the Github and Zenodo releases:
version: 1.1.01
DOI: 10.5281/zenodo.4147144

[mikldk]

@whedon set 10.5281/zenodo.4147144 as archive

[whedon]

OK. 10.5281/zenodo.4147144 is the archive.

[mikldk]

@VincentAlcazer I apologise for being pedantic, but 1.1.01 is not a valid semantic version number, which I strongly suggest to stick to. See https://semver.org/ under §2 ("A normal version number MUST take the form X.Y.Z where X, Y, and Z are non-negative integers, and MUST NOT contain leading zeroes.").

I would suggest calling it version 1.1.1 instead.

[VincentAlcazer]

@mikldk I understand and sorry for this fastidious release. In fact I chose 1.1.01 due to Zenodo conflicts for 1.1.1.

I updated the version (and had to change the number for Zenodo):
New version: 1.1.2
10.5281/zenodo.4152933

Thank you again for your time.

Best regards,

Vincent Alcazer

[mikldk]

@whedon set 10.5281/zenodo.4152933 as archive

[whedon]

OK. 10.5281/zenodo.4152933 is the archive.

[mikldk]

@whedon set v1.1.2 as version

[whedon]

OK. v1.1.2 is the version.

[mikldk]

@whedon generate pdf

[whedon]

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

[mikldk]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.18637/jss.v014.i09 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#1878

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1878, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[mikldk]

@nistara, @adithirgis Thank you very much for your effort in reviewing this paper!

[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.02630 joss-papers#1881
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02630
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]

@nistara, @adithirgis - many thanks for your reviews here and to @mikldk for editing this submission ✨

@VincentAlcazer - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

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

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reStructuredText:
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This is how it will look in your documentation:

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