[REVIEW]: MiscMetabar: an R package to facilitate visualization and Reproducibility in metabarcoding analysis #6038

editorialbot · 2023-11-08T17:57:04Z

Submitting author: @adrientaudiere (Adrien Taudiere)
Repository: https://github.com/adrientaudiere/MiscMetabar
Branch with paper.md (empty if default branch):
Version: v0.52
Editor: @kellyrowland
Reviewers: @tkchafin, @iimog
Archive: 10.5281/zenodo.10370781

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/6ed7964db44853c0b2f942483763e6d3/status.svg)](https://joss.theoj.org/papers/6ed7964db44853c0b2f942483763e6d3)

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

@tkchafin & @iimog, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kellyrowland 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 ✨

Checklists

📝 Checklist for @tkchafin

📝 Checklist for @iimog

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-11-08T17:57:06Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot · 2023-11-08T17:57:12Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (641.8 files/s, 246960.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             12              3              3          16193
R                               36            715           2438           5791
Markdown                         8            325              0           1024
TeX                              2             62              0            652
Rmd                              9            175            309            214
YAML                             4             21             10            138
CSS                              1              1              0              9
JSON                             1              0              0              7
-------------------------------------------------------------------------------
SUM:                            73           1302           2760          24028
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-11-08T17:57:14Z

Wordcount for paper.md is 1024

editorialbot · 2023-11-08T17:57:24Z

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

OK DOIs

- 10.32388/rhq6vj is OK
- 10.21105/joss.03201 is OK
- 10.1038/s41587-019-0209-9 is OK
- 10.21105/joss.03201 is OK
- 10.1038/nmeth.3869 is OK
- 10.18129/B9.bioc.mia is OK
- 10.1038/s41467-017-01312-x is OK
- 10.21105/joss.02959 is OK
- 10.21203/rs.3.rs-2011054/v1 is OK
- 10.5281/zenodo.3923184 is OK
- 10.1371/journal.pone.0061217 is OK
- 10.1016/j.funeco.2019.03.005 is OK
- 10.1186/s40104-022-00725-z is OK
- 10.1128/aem.02343-19 is OK
- 10.21105/joss.01442 is OK
- 10.1002/(issn)2637-4943 is OK
- 10.22541/au.163430390.04226544/v1 is OK
- 10.1016/j.tree.2008.09.011 is OK
- 10.1007/s00248-021-01833-5 is OK
- 10.1016/j.xinn.2023.100388 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-11-08T17:58:23Z

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

tkchafin · 2023-11-08T18:04:28Z

Review checklist for @tkchafin

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 https://github.com/adrientaudiere/MiscMetabar?
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 (@adrientaudiere) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
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?

Kevin-Mattheus-Moerman · 2023-12-04T16:12:48Z

@iimog thanks for your help with this review. Are you able to get started as well? You can do so by generating the checklist by calling: @editorialbot generate my checklist

iimog · 2023-12-05T10:56:55Z

Hi @Kevin-Mattheus-Moerman, thank you for the reminder. I already read the paper and started looking into the code. I'll also officially start my review now 🙂

@editorialbot generate my checklist

iimog · 2023-12-05T10:57:37Z

Review checklist for @iimog

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 https://github.com/adrientaudiere/MiscMetabar?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@adrientaudiere) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
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?

tkchafin · 2023-12-06T13:16:52Z

@Kevin-Mattheus-Moerman I've completed my review. I have posted some minor issues regarding the installation instructions and missing dependencies, which I expect will be easy to resolve. I've also posted some minor editorial notes for the paper (typos and small grammatical corrections). Once these are resolved I can check off the final item in my checklist!

adrientaudiere · 2023-12-06T15:06:19Z

@editorialbot generate pdf

editorialbot · 2023-12-06T15:07:34Z

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

tkchafin · 2023-12-06T16:10:09Z

Just to update, the author has addressed all of the issues mentioned above, so I've completed my checklist

kellyrowland · 2023-12-13T17:26:41Z

@editorialbot set v0.52 as version

editorialbot · 2023-12-13T17:26:43Z

Done! version is now v0.52

kellyrowland · 2023-12-13T17:27:11Z

@editorialbot recommend-accept

editorialbot · 2023-12-13T17:27:12Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-12-13T17:28:28Z

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

OK DOIs

- 10.32388/rhq6vj is OK
- 10.21105/joss.03201 is OK
- 10.1038/s41587-019-0209-9 is OK
- 10.21105/joss.03201 is OK
- 10.1038/nmeth.3869 is OK
- 10.18129/B9.bioc.mia is OK
- 10.1038/s41467-017-01312-x is OK
- 10.21105/joss.02959 is OK
- 10.21203/rs.3.rs-2011054/v1 is OK
- 10.21203/rs.3.rs-2011054/v1 is OK
- 10.5281/zenodo.3923184 is OK
- 10.1371/journal.pone.0061217 is OK
- 10.1016/j.funeco.2019.03.005 is OK
- 10.1186/s40104-022-00725-z is OK
- 10.1128/aem.02343-19 is OK
- 10.21105/joss.01442 is OK
- 10.1002/(issn)2637-4943 is OK
- 10.22541/au.163430390.04226544/v1 is OK
- 10.1016/j.tree.2008.09.011 is OK
- 10.1007/s00248-021-01833-5 is OK
- 10.1016/j.xinn.2023.100388 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-12-13T17:28:42Z

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4837, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2023-12-15T17:42:20Z

@adrientaudiere As AEiC I will now help process this work for acceptance. I have checked this review, the paper, the repository, and the archive link. Most seems in order, I do however have the below points that need your attention.

On the archive:

Note, it is not a requirement, but we recommend that you add the ORCID link for the author listed on the ZENODO archive.

On the paper:

The paper title currently contains: MiscMetabar : an R packages..., this should probably be edited to: MiscMetabar: an R package..., or else MiscMetabar: R packages... if it does refer to multiple. Note I also removed the space between the project name and :.

Missing DOIs:

10.1093/nar/gkaa434 for:

Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., &
Nekrutenko, A. (2020). The galaxy platform for accessible, reproducible and collaborative
biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402.

10.1186/1471-2105-12-385 for:

Ondov, B.D., Bergman, N.H. & Phillippy, A.M. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12, 385 (2011).

10.1128/spectrum.01978-23 for:

Vieira, F. R., Di Tomassi, I., O’Connor, E., Bull, C. T., Pecchia, J. A., & Hockett, K. L.
(2023). Manipulating agaricus bisporus developmental patterns by passaging microbial
communities in complex substrates. Microbiology Spectrum, e01978–23.

10.1093/procel/pwad024 for:

Wen, T., Niu, G., Chen, T., Shen, Q., Yuan, J., & Liu, Y.-X. (2023). The best practice for
microbiome analysis using r. Protein & Cell, pwad024

Kevin-Mattheus-Moerman · 2023-12-18T11:14:03Z

@adrientaudiere 👋

adrientaudiere · 2023-12-18T13:20:05Z

@editorialbot generate pdf

editorialbot · 2023-12-18T13:21:24Z

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

adrientaudiere · 2023-12-18T13:28:00Z

Thanks @Kevin-Mattheus-Moerman. Two errors in the title, I'm a bit ashamed… Title and doi must be ok this time. I also add my orcid number in zenodo.

adrientaudiere · 2023-12-18T18:58:34Z

@editorialbot check references

editorialbot · 2023-12-18T18:58:56Z

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

OK DOIs

- 10.32388/rhq6vj is OK
- 10.21105/joss.03201 is OK
- 10.1038/s41587-019-0209-9 is OK
- 10.21105/joss.03201 is OK
- 10.1038/nmeth.3869 is OK
- 10.18129/B9.bioc.mia is OK
- 10.1038/s41467-017-01312-x is OK
- 10.1093/nar/gkaa434 is OK
- 10.21105/joss.02959 is OK
- 10.21203/rs.3.rs-2011054/v1 is OK
- 10.21203/rs.3.rs-2011054/v1 is OK
- 10.5281/zenodo.3923184 is OK
- 10.1371/journal.pone.0061217 is OK
- 10.1186/1471-2105-12-385 is OK
- 10.1016/j.funeco.2019.03.005 is OK
- 10.1186/s40104-022-00725-z is OK
- 10.1128/aem.02343-19 is OK
- 10.21105/joss.01442 is OK
- 10.1002/(issn)2637-4943 is OK
- 10.22541/au.163430390.04226544/v1 is OK
- 10.1016/j.tree.2008.09.011 is OK
- 10.1007/s00248-021-01833-5 is OK
- 10.1128/spectrum.01978-23 is OK
- 10.1093/procel/pwad024 is OK
- 10.1016/j.xinn.2023.100388 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2023-12-19T09:08:58Z

@adrientaudiere thanks for fixing those aspects. One more thing:

please can you edit the ZENODO archive title to match the paper title? Thanks!

adrientaudiere · 2023-12-19T09:14:05Z

Done. I also put the R of reproducibility in lowercase, like in the paper title.

MiscMetabar: an R package to facilitate visualization and reproducibility in metabarcoding analysis

Kevin-Mattheus-Moerman · 2023-12-19T12:17:45Z

@editorialbot accept

editorialbot · 2023-12-19T12:17:47Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2023-12-19T12:19:58Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Taudière
  given-names: Adrien
  orcid: "https://orcid.org/0000-0003-1088-1182"
doi: 10.5281/zenodo.10370781
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Taudière
    given-names: Adrien
    orcid: "https://orcid.org/0000-0003-1088-1182"
  date-published: 2023-12-19
  doi: 10.21105/joss.06038
  issn: 2475-9066
  issue: 92
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6038
  title: "MiscMetabar: an R package to facilitate visualization and
    reproducibility in metabarcoding analysis"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06038"
  volume: 8
title: "MiscMetabar: an R package to facilitate visualization and
  reproducibility in metabarcoding analysis"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2023-12-19T12:20:03Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-12-19T12:20:04Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06038 joss-papers#4855
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06038
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kellyrowland · 2024-01-08T18:50:33Z

@Kevin-Mattheus-Moerman I think this can be closed? not sure if that is supposed to be automatic upon publication.

Kevin-Mattheus-Moerman · 2024-01-11T16:54:33Z

@kellyrowland that happens manually. Sorry I was out for the holidays. Back now and will close this now as the DOI resolves. Thanks.

Kevin-Mattheus-Moerman · 2024-01-11T16:55:05Z

@adrientaudiere congratulations on this publications!

Thanks for editing @kellyrowland, and a special thanks to the reviewers: @tkchafin, @iimog !!

editorialbot · 2024-01-11T16:55:07Z

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

If you would like to include a link to your paper from your README use the following code snippets:

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  <img src="https://joss.theoj.org/papers/10.21105/joss.06038/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06038/status.svg
   :target: https://doi.org/10.21105/joss.06038

This is how it will look in your documentation:

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editorialbot added CSS R review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Nov 8, 2023

editorialbot assigned kellyrowland Nov 8, 2023

editorialbot mentioned this issue Nov 8, 2023

[PRE REVIEW]: MiscMetabar : a R packages to facilitate visualization and Reproducibility in metabarcoding analysis #5977

Closed

Kevin-Mattheus-Moerman removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Dec 4, 2023

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 13, 2023

Kevin-Mattheus-Moerman changed the title ~~[REVIEW]: MiscMetabar : a R packages to facilitate visualization and Reproducibility in metabarcoding analysis~~ [REVIEW]: MiscMetabar: an R package to facilitate visualization and Reproducibility in metabarcoding analysis Dec 19, 2023

editorialbot added accepted published Papers published in JOSS labels Dec 19, 2023

Kevin-Mattheus-Moerman closed this as completed Jan 11, 2024

editorialbot mentioned this issue Dec 17, 2024

[PRE REVIEW]: funkyheatmap: Visualising data frames with mixed data types #7590

Open

[REVIEW]: MiscMetabar: an R package to facilitate visualization and Reproducibility in metabarcoding analysis #6038

[REVIEW]: MiscMetabar: an R package to facilitate visualization and Reproducibility in metabarcoding analysis #6038

Comments

editorialbot commented Nov 8, 2023 • edited Loading

Status

Reviewer instructions & questions

Checklists

editorialbot commented Nov 8, 2023

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tkchafin commented Nov 8, 2023 • edited Loading

Review checklist for @tkchafin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Kevin-Mattheus-Moerman commented Dec 4, 2023

iimog commented Dec 5, 2023

iimog commented Dec 5, 2023 • edited Loading

Review checklist for @iimog

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

tkchafin commented Dec 6, 2023

adrientaudiere commented Dec 6, 2023

editorialbot commented Dec 6, 2023

tkchafin commented Dec 6, 2023 • edited Loading

kellyrowland commented Dec 13, 2023

editorialbot commented Dec 13, 2023

kellyrowland commented Dec 13, 2023

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Kevin-Mattheus-Moerman commented Dec 15, 2023 • edited Loading

Kevin-Mattheus-Moerman commented Dec 18, 2023

adrientaudiere commented Dec 18, 2023

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adrientaudiere commented Dec 18, 2023

adrientaudiere commented Dec 18, 2023

editorialbot commented Dec 18, 2023

Kevin-Mattheus-Moerman commented Dec 19, 2023 • edited Loading

adrientaudiere commented Dec 19, 2023

Kevin-Mattheus-Moerman commented Dec 19, 2023

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kellyrowland commented Jan 8, 2024

Kevin-Mattheus-Moerman commented Jan 11, 2024

Kevin-Mattheus-Moerman commented Jan 11, 2024

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editorialbot commented Nov 8, 2023 •

edited

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tkchafin commented Nov 8, 2023 •

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