[REVIEW]: microViz: an R package for microbiome data visualization and statistics

[whedon]

Submitting author: @david-barnett (David Barnett)
Repository: https://github.com/david-barnett/microViz
Version: v0.7.9
Editor: @lpantano
Reviewers: @marypiper, @yoonjeongcha
Archive: 10.5281/zenodo.5048013

⚠️ 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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4547b492f224a26d96938ada81fee3fa"><img src="https://joss.theoj.org/papers/4547b492f224a26d96938ada81fee3fa/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4547b492f224a26d96938ada81fee3fa/status.svg)](https://joss.theoj.org/papers/4547b492f224a26d96938ada81fee3fa)

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

@marypiper, @yoonjeongcha, 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 @lpantano 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 @yoonjeongcha

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 (@david-barnett) 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 @marypiper

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 (@david-barnett) 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. @marypiper 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=0.53 s (204.0 files/s, 33104.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               76            551           3322           4590
SVG                              1              0              0           2852
Markdown                        14            559              0           2642
JSON                             5             25              0           1669
Rmd                              6            255            423            398
YAML                             5             45              6            242
TeX                              1             11              0             95
Dockerfile                       1              1              0              2
-------------------------------------------------------------------------------
SUM:                           109           1447           3751          12490
-------------------------------------------------------------------------------


Statistical information for the repository '52516f282deb4a62252abeca' was
gathered on 2021/04/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
David Barnett                    4           496            496          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

[whedon]

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

OK DOIs

- 10.21105/joss.01686 is OK
- 10.1371/journal.pcbi.1005404 is OK
- 10.1371/journal.pone.0061217 is OK
- 10.1111/2041-210X.12628 is OK
- 10.1214/19-AOAS1283 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[lpantano]

@whedon add @yoonjeongcha as reviewer

[whedon]

OK, @yoonjeongcha is now a reviewer

[whedon]

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

[marypiper]

@whedon commands

…

On Wed, May 5, 2021 at 4:31 PM whedon ***@***.***> wrote: 👋 @marypiper <https://github.com/marypiper>, please update us on how your review is going (this is an automated reminder). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3201 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABYSJABM4XFNAALEC6DNYL3TMGTLHANCNFSM43LCXCLQ> .

[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

[marypiper]

@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

[marypiper]

@whedon generate pdf

[whedon]

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

[marypiper]

@lpantano, do I comment on small issues with the paper here and larger issues submit an issue and comment here a link to the issue?

[lpantano]

@marypiper, you can create all the issues (or one with all the comments) in their repository and then make a comment here mentioning all the issues you created, so it is easy to see when they get closed. Thanks!

[david-barnett]

Hi all,

Firstly, many thanks to marypiper and yoonjeongcha for agreeing to review my work 🙂

Secondly, over the last couple of weeks I have made some, mostly small, changes to microViz in response to user requests and reports, which are listed in the changelog

Should I / can I somehow update the version in Whedon's comment to the current version? 0.7.5

[lpantano]

@david-barnett , thanks for the update. We can change the version towards the end, when we are sure no more changes are needed. I will ask at the very end of the process this information together with few other. Thanks!

[lpantano]

Hi @yoonjeongcha,@marypiper, I see you are working on this recently. Can you give us an update on this? if you are waiting from authors or still working on checking the different items in the checklist. Thanks!

[marypiper]

@lpantano, I am still working on the review.

[lpantano]

@whedon generate pdf

[whedon]

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

[lpantano]

@whedon check references

[whedon]

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

OK DOIs

- 10.21105/joss.01686 is OK
- 10.1371/journal.pcbi.1005404 is OK
- 10.1371/journal.pone.0061217 is OK
- 10.1111/2041-210X.12628 is OK
- 10.1214/19-AOAS1283 is OK
- 10.1093/bioinformatics/bts342 is OK
- 10.3389/fmicb.2017.02224 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[lpantano]

Thank you @yoonjeongcha and @marypiper for your time!

@david-barnett, At this point could you:

• Make a tagged release of your software, and list the version tag of the archived version here. (or point to the current one if it is done already)
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[david-barnett]

Great! 🙂 and thank you all so much for volunteering your time

@lpantano here is the latest tagged release and the Zenodo archive, I hope this is all in order
https://github.com/david-barnett/microViz/releases/tag/0.7.9
https://doi.org/10.5281/zenodo.5048013

[lpantano]

@whedon set v0.7.9 as version

[whedon]

OK. v0.7.9 is the version.

[lpantano]

@david-barnett, thank you for the link. A final detail is that the zenodo archive has to match the title and the authors as they appear in the paper. I think that would be the only modification needed. Thanks!

[david-barnett]

ah yes, okay I have fixed that now, thanks @lpantano. https://zenodo.org/record/5048013

[lpantano]

@whedon set 10.5281/zenodo.5048013 as archive

[whedon]

OK. 10.5281/zenodo.5048013 is the archive.

[lpantano]

@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

- 10.21105/joss.01686 is OK
- 10.1371/journal.pcbi.1005404 is OK
- 10.1371/journal.pone.0061217 is OK
- 10.1111/2041-210X.12628 is OK
- 10.1214/19-AOAS1283 is OK
- 10.1093/bioinformatics/bts342 is OK
- 10.3389/fmicb.2017.02224 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#2435

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2435, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[Kevin-Mattheus-Moerman]

@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.03201 joss-papers#2441
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03201
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...

[Kevin-Mattheus-Moerman]

Congratulations @david-barnett on your accepted paper!

Thank you @lpantano for editing this work!

And a special thanks to the reviewers @marypiper and @yoonjeongcha!!!

[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.03201/status.svg)](https://doi.org/10.21105/joss.03201)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03201">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03201/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03201/status.svg
   :target: https://doi.org/10.21105/joss.03201

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss