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[REVIEW]: microViz: an R package for microbiome data visualization and statistics #3201

Closed whedon closed 3 years ago

whedon commented 3 years ago

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

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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:

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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

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @marypiper

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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 :tada:.

:warning: JOSS reduced service mode :warning:

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 commented 3 years ago 
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 commented 3 years ago 
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 commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lpantano commented 3 years ago

@whedon add @yoonjeongcha as reviewer

whedon commented 3 years ago

OK, @yoonjeongcha is now a reviewer

whedon commented 3 years ago

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

marypiper commented 3 years ago

@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 https://github.com/openjournals/joss-reviews/issues/3201#issuecomment-832987178, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABYSJABM4XFNAALEC6DNYL3TMGTLHANCNFSM43LCXCLQ .

whedon commented 3 years ago

Here are some things you can ask me to do:

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@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 commented 3 years ago

@whedon commands

whedon commented 3 years ago

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 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

marypiper commented 3 years ago

@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 commented 3 years ago

@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 commented 3 years ago

Hi all,

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

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 commented 3 years ago

@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 commented 3 years ago

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 commented 3 years ago

@lpantano, I am still working on the review.

marypiper commented 3 years ago

Hi @david-barnett, just wanted to let you know that I have posted a couple of issues related to questions I had regarding the statement of need (https://github.com/david-barnett/microViz/issues/26) and the functionality of the RShiny app (https://github.com/david-barnett/microViz/issues/25). Thanks!

yoonjeongcha commented 3 years ago

Hi all, I am also still working on the review.

david-barnett commented 3 years ago

Hi @david-barnett, just wanted to let you know that I have posted a couple of issues related to questions I had regarding the statement of need (david-barnett/microViz#26) and the functionality of the RShiny app (david-barnett/microViz#25). Thanks!

Thanks for raising these issues marypiper, I have taken actions to address your points, and I included descriptions of the changes I have made directly on the relevant issues. Do let me know if there is more to be done. Thanks!

marypiper commented 3 years ago

@lpantano, I have completed my review of microViz. I initially had issues testing out the interactive component of microViz and had questions regarding the novelty of the functions. However, @david-barnett addressed these, fixing the interactive visualizations so that they now function appropriately and he has provided additional documentation for users. David has provided the updated reference for the microbiome citation, and he has provided more explanations regarding the usefulness of his contributions. While the methods proposed aren't in and of themselves novel, he has brought together useful functions from quite a few microbiome analysis packages and provided wrappers to make them easier to use, especially for a more novice R user working to perform visualizations of their microbiome data. David has created useful visualizations that are aesthetically pleasing and often not available in the main packages for microbiome data analysis/visualization, in addition to providing the ordination plots as an interactive RShiny package.

lpantano commented 3 years ago

@yoonjeongcha, do you think you could wrap up this in the next week or give a timeline? thanks!

yoonjeongcha commented 3 years ago

Yes, I can definitely do that! I have to admit this is my first time reviewing a package so I'm not sure I'll catch any additional issues, but I will try my best!

lpantano commented 3 years ago

@yoonjeongcha, that is totally fine. That happens a lot, where all the requirements are already fulfilled. Thank you for your time.

yoonjeongcha commented 3 years ago

@lpantano, I am now also done with my review. The visualization and interactive exploration were easy to use and helpful. The code was clean and well documented, and the vignettes had great examples. The tutorials and video were also well made. Overall I thought it was a great package for those who want to explore and visualize microbiome sequencing data in a single package.

lpantano commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lpantano commented 3 years ago

@whedon check references

whedon commented 3 years ago 
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 commented 3 years ago

Thank you @yoonjeongcha and @marypiper for your time!

@david-barnett, At this point could you:

I can then move forward with accepting the submission.

david-barnett commented 3 years ago

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 commented 3 years ago

@whedon set v0.7.9 as version

whedon commented 3 years ago

OK. v0.7.9 is the version.

lpantano commented 3 years ago

@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 commented 3 years ago

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

lpantano commented 3 years ago

@whedon set 10.5281/zenodo.5048013 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5048013 is the archive.

lpantano commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
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 commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2435

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2441
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03201
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 3 years ago

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 commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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   :target: https://doi.org/10.21105/joss.03201

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