[REVIEW]: FielDHub: An R Shiny Package for Design of Experiments in Life Sciences

[whedon]

Submitting author: @DidierMurilloF (Didier Murillo Florez)
Repository: https://github.com/DidierMurilloF/FielDHub
Version: v0.1.0
Editor: @csoneson
Reviewer: @Prof-ThiagoOliveira, @dlebauer
Archive: 10.5281/zenodo.4768611

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Status

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Markdown: [![status](https://joss.theoj.org/papers/c686579ab789fb4340baef052d3bf311/status.svg)](https://joss.theoj.org/papers/c686579ab789fb4340baef052d3bf311)

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

@Prof-ThiagoOliveira & @dlebauer, 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

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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 @Prof-ThiagoOliveira

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 (@DidierMurilloF) 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 @dlebauer

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 (@DidierMurilloF) 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. @Prof-ThiagoOliveira, @dlebauer 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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.27 s (490.4 files/s, 102676.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            30           1365            357          10628
R                               81           1774           1785           9884
CSS                              5            148             70            642
JavaScript                       3             64             32            256
Markdown                         5             72              0            182
TeX                              1              5              0             51
YAML                             4              4              3             43
SVG                              1              0              1             11
Rmd                              1             12             31              6
-------------------------------------------------------------------------------
SUM:                           131           3444           2279          21703
-------------------------------------------------------------------------------


Statistical information for the repository '0760439efd04e1b7cebeea64' was
gathered on 2021/03/18.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
DidierMurillo                    1           352              0          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
DidierMurillo               352          100.0          0.0                9.09

[whedon]

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

OK DOIs

- 10.1111/j.1467-842X.2011.00642.x is OK
- 10.1198/108571106X154443 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[csoneson]

👋 @DidierMurilloF, @Prof-ThiagoOliveira, @dlebauer - this is the review thread for the submission. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread. 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 directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

[dlebauer]

PR submitted w/ OSI approved license DidierMurilloF/FielDHub#1

[Prof-ThiagoOliveira]

I've been submitting issues with partial solutions to #3107

Issue 2 - DidierMurilloF/FielDHub#2
Issue 3 - DidierMurilloF/FielDHub#3
Issue 4 - DidierMurilloF/FielDHub#4

[Prof-ThiagoOliveira]

PR submitted with changes DidierMurilloF/FielDHub#5

[Prof-ThiagoOliveira]

PR submitted with changes on fct_full_factorial.R. DidierMurilloF/FielDHub#6

[Prof-ThiagoOliveira]

Issue 7 - DidierMurilloF/FielDHub#7

[Prof-ThiagoOliveira]

Issue 8 - DidierMurilloF/FielDHub#8

[Prof-ThiagoOliveira]

Issue 9 - DidierMurilloF/FielDHub#9

[Prof-ThiagoOliveira]

Issue 10 - DidierMurilloF/FielDHub#10

[Prof-ThiagoOliveira]

Issue 11 - DidierMurilloF/FielDHub#11

[csoneson]

Hi all - just wanted to check in to see how things are going. I see that @Prof-ThiagoOliveira has submitted a number of issues that are being actively worked on. @dlebauer - could you give us a quick update on where things are on your side? Just ping me if there are any questions. Thanks!

[whedon]

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

[whedon]

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

[Prof-ThiagoOliveira]

@csoneson I am waiting for the authors to update my suggestions. Where could I include suggestions about the manuscript?

[csoneson]

Thanks @Prof-ThiagoOliveira! You can add comments on theh paper either as posts in this thread or open an issue in the software repository as you have done above.

[csoneson]

@dlebauer - could you update us on how your review is going? Thanks!

[dlebauer]

@csoneson this is my first review for JOSS. Just learning how this works. One of the first things I usually do when reviewing an article is see if it meets journal requirements. In this case I started by submitting a pr to meet the journal requirements of having an OSI approved license see #3122 (comment). However it hasn't been merged or addressed (eg with a different license). While this doesn't prevent a full review, I was hoping this would be a first step and would establish the pattern for using issues and prs as a mechanism for review as suggested by JOSS, and which I think is a great idea.

[csoneson]

Thanks @dlebauer. From the DESCRIPTION file it looks like the package is indeed MIT licensed. @DidierMurilloF - could you clarify the situation here (and add the license to the repository as well)?

[DidierMurilloF]

@whedon generate pdf

[whedon]

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

[DidierMurilloF]

Dear @csoneson,

Thank you for your help. I got all steps listed above. Now FielDHub is available at Zenodo.

The corresponding DOI is the following,

https://zenodo.org/record/4768611

I also did small changes to the title of the paper to match with the release at R CRAN. Thank you!

Best,

Didier Murillo.

[csoneson]

@whedon set 10.5281/zenodo.4768611 as archive

[whedon]

OK. 10.5281/zenodo.4768611 is the archive.

[csoneson]

@whedon set v0.1.0 as version

[whedon]

OK. v0.1.0 is the version.

[csoneson]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1111/j.1467-842X.2011.00642.x is OK
- 10.1198/108571106X154443 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#2316

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2316, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[csoneson]

Thanks @DidierMurilloF! I'm handing over now to the Associate Editor in Chief on rotation for the final steps.

[DidierMurilloF]

Dear @csoneson thank you very much for all your help. We look forward to hearing more about the next steps.

Best regards,

Didier Murillo

[kyleniemeyer]

Hi @DidierMurilloF, I'm the AEIC on duty this week doing some final checks before publishing. I noticed some minor issues in the references, could you merge this PR I made to fix them? DidierMurilloF/FielDHub#16

[DidierMurilloF]

Dear @kyleniemeyer thank you for your help! I merged the pull request. Please, let me know if you need anything else from me.

Best,

Didier Murillo.

[kyleniemeyer]

@whedon generate pdf

[whedon]

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

[kyleniemeyer]

@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.03122 joss-papers#2320
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03122
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...

[kyleniemeyer]

Congrats @DidierMurilloF on your article's publication in JOSS!

Many thanks to @Prof-ThiagoOliveira and @dlebauer for reviewing this, and @csoneson for editing.

[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:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03122/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03122/status.svg
   :target: https://doi.org/10.21105/joss.03122

This is how it will look in your documentation:

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