[REVIEW]: morse: an R-package in support of Environmental Risk Assessment

whedon commented 3 years ago

Submitting author: @sandrinecharles (Sandrine CHARLES) Repository: https://github.com/pveber/morse Version: v3.1.0 Editor: @KristinaRiemer Reviewers: @puruckertom, @Peter-Vermeiren Archive: 10.5281/zenodo.5771022

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Status

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Markdown: [![status](https://joss.theoj.org/papers/1625fe55480a11b31989d7306f41e8f4/status.svg)](https://joss.theoj.org/papers/1625fe55480a11b31989d7306f41e8f4)

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

@BrandonEdwards & @puruckertom, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @KristinaRiemer 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 @puruckertom

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 repository url?
[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 (@sandrinecharles) 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

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] #3734
[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 and who the target audience is?
[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?

Review checklist for @Peter-Vermeiren

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 repository url?
[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 (@sandrinecharles) 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

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] #3903
[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 and who the target audience is?
[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?

KristinaRiemer commented 2 years ago

@whedon set 10.5281/zenodo.5771022 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5771022 is the archive.

KristinaRiemer commented 2 years ago

@whedon set v3.1.0 as version

whedon commented 2 years ago

OK. v3.1.0 is the version.

KristinaRiemer commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

OK DOIs

- 10.1021/es801418x is OK
- 10.1021/es502009r is OK
- 10.1787/9789264085275-en is OK
- 10.1787/9789264264335-en is OK
- 10.1787/9789264304741-12-en is OK
- 10.1007/s11356-017-9809-4 is OK
- 10.1021/acs.est.7b05464 is OK
- 10.1038/s41598-019-47698-0 is OK
- 10.2903/j.efsa.2018.5377 is OK
- 10.1002/ieam.4061 is OK
- 10.1007/s10646-012-0917-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

KristinaRiemer commented 2 years ago

@sandrinecharles your submission is now going to be passed along to an EiC, who will do some final checks before publication.

whedon commented 2 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/2817

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2817, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 2 years ago

@sandrinecharles - I've suggested a bunch of changes in https://github.com/pveber/morse/pull/292 - please merge this (or let me know what you disagree with), then run @whedon generate pdf to make sure everything still looks good to you, and let me know when you are ready to proceed to publication

sandrinecharles commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

sandrinecharles commented 2 years ago

@danielskatz A last edit change is needed at line 127: "We will used the reduced version" --> "We will use the reduced version"

danielskatz commented 2 years ago

Please go ahead and make that change, then let me know

sandrinecharles commented 2 years ago

Please go ahead and make that change, then let me know

done, in push to https://github.com/pveber/morse/tree/master/paper

danielskatz commented 2 years ago

@whedon generate pdf

sandrinecharles commented 2 years ago

@danielskatz argh sorry I did a big mistake!!! I used the old paper.md file :-( I am stupid. How to repare this?

whedon commented 2 years ago

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

danielskatz commented 2 years ago

@sandrinecharles - you can go back to https://github.com/pveber/morse/blob/a5ed566cd4d9849b2105bd9b05c757a6d2f92be1/paper/paper.md and make the appropriate edit there

sandrinecharles commented 2 years ago

@danielskatz thanks, it is repaired!

danielskatz commented 2 years ago

@whedon generate pdf

@sandrinecharles - please confirm the results of this are correct, then we'll proceed

whedon commented 2 years ago

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

sandrinecharles commented 2 years ago

please confirm the results of this are correct, then we'll proceed

I confirm.

danielskatz commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago

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

whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/2820
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03200
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 2 years ago

Congratulations to @sandrinecharles (Sandrine CHARLES) and co-author!!

And thanks to @puruckertom and @Peter-Vermeiren for reviewing, and to @KristinaRiemer for editing! We couldn't do this without you

whedon commented 2 years ago

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

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.03200/status.svg)](https://doi.org/10.21105/joss.03200)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03200">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03200/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03200/status.svg
   :target: https://doi.org/10.21105/joss.03200

This is how it will look in your documentation:

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sandrinecharles commented 2 years ago

Congratulations to @sandrinecharles (Sandrine CHARLES) and co-author!!

And thanks to @puruckertom and @Peter-Vermeiren for reviewing, and to @KristinaRiemer for editing! We couldn't do this without you

What a nice Christmas gift! Thank you very much to all of you for making this paper published.

KristinaRiemer commented 2 years ago

@sandrinecharles thank you for your patience with this process, and congratulations!

sandrinecharles commented 2 years ago

@KristinaRiemer Dear Kristina, we juste finalised a new paper that we would also like to submit to JOSS, on a new package developed this year: https://CRAN.R-project.org/package=rbioacc, in support of a dedicated Shiny tool available fro free online: http://lbbe-shiny.univ-lyon1.fr/mosaic-bioacc/. Would you be interested in taking care of the reviewing process for this paper. Peter Vermeiren could be one the reviewer, as the philosophy is really the same as in 'morse'. I could also suggest to ask Benoît Goussen from Section Head Ecological Modelling, ibacon GmbH, in Germany. Our preprint is already within bioRxiv here: https://www.biorxiv.org/content/10.1101/2021.09.08.459421v2, and our Git repository here: https://gitlab.in2p3.fr/sandrine.charles/rbioacc

kthyng commented 2 years ago

@sandrinecharles In case you haven't already done so, please just go ahead and submit your new JOSS paper and you can select @KristinaRiemer as the suggested editor. Please include your reviewer suggestion.

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