editorialbot commented 10 months ago

Submitting author: !--author-handle-->@adrientaudiere@kellyrowland<!--end-editor-- Reviewers: @tkchafin, @iimog Archive: 10.5281/zenodo.10370781

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6ed7964db44853c0b2f942483763e6d3"><img src="https://joss.theoj.org/papers/6ed7964db44853c0b2f942483763e6d3/status.svg"></a>
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:

@editorialbot generate my checklist

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

editorialbot commented 10 months ago

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

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot commented 10 months ago

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 commented 10 months ago

Wordcount for paper.md is 1024

editorialbot commented 10 months ago

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 commented 10 months ago

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

tkchafin commented 10 months ago

Review checklist for @tkchafin

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/adrientaudiere/MiscMetabar?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 9 months ago

@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 commented 9 months ago

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 :slightly_smiling_face:

@editorialbot generate my checklist

iimog commented 9 months ago

Review checklist for @iimog

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/adrientaudiere/MiscMetabar?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 9 months ago

@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 commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

tkchafin commented 9 months ago

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

iimog commented 9 months ago

Update from my side: I went through the manuscript and the repository. My general impression is, that MiscMetabar is a mature R package with a lot of useful functionality. @adrientaudiere put a lot of effort into development, testing, and documentation. I found a couple of minor issues, that are linked to this thread. I'm happy to re-evaluate and tick off the remaining boxes, as soon as they are addressed.

adrientaudiere commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

adrientaudiere commented 9 months ago

@editorialbot generate pdf

adrientaudiere commented 9 months ago

@editorialbot commands

editorialbot commented 9 months ago

Hello @adrientaudiere, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

adrientaudiere commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

editorialbot commented 9 months ago

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

- 10.1038/s41467-023-39876-6 may be a valid DOI for title: Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations

INVALID DOIs

- None

iimog commented 9 months ago

All of my issues have already been addressed and resolved :+1:

adrientaudiere commented 9 months ago

Thanks a lot @iimog @tkchafin for your review. It drastically improves the code and helps a lot improving the paper and the package.

adrientaudiere commented 9 months ago

@editorialbot check references

adrientaudiere commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

- 10.1038/s41467-023-39876-6 may be a valid DOI for title: Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations

INVALID DOIs

- None

editorialbot commented 9 months ago

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

adrientaudiere commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

- 10.1038/s41467-023-39876-6 may be a valid DOI for title: Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations

INVALID DOIs

- None

adrientaudiere commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

- 10.1038/s41467-023-39876-6 may be a valid DOI for title: Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations

INVALID DOIs

- None

kellyrowland commented 9 months ago

@adrientaudiere it looks like we're just about ready to start wrapping up the review; I'll post some next steps once that last DOI is in place. thanks!

adrientaudiere commented 9 months ago

@editorialbot generate pdf

adrientaudiere commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

- 10.1038/s41467-023-39876-6 may be a valid DOI for title: Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations

INVALID DOIs

- None

editorialbot commented 9 months ago

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

adrientaudiere commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

adrientaudiere commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

kellyrowland commented 9 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

kellyrowland commented 9 months ago

@adrientaudiere please:

Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.

You won't be able to check off the related items in the above checklist that I just generated; I'll check them once things have been completed.

adrientaudiere commented 9 months ago

Hi @kellyrowland, This is done for v. 0.52 : zenodo doi : 10.5281/zenodo.10370781

kellyrowland commented 9 months ago

@editorialbot set archive as 10.5281/zenodo.10370781

editorialbot commented 9 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

kellyrowland commented 9 months ago

@editorialbot set 10.5281/zenodo.10370781 as archive

editorialbot commented 9 months ago

Done! archive is now 10.5281/zenodo.10370781

kellyrowland commented 9 months ago

@editorialbot set v0.52 as version

editorialbot commented 9 months ago

Done! version is now v0.52

openjournals / joss-reviews

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

Status

Reviewer instructions & questions

Checklists

Review checklist for @tkchafin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @iimog

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance