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[REVIEW]: simode: R Package for Statistical Inference of Ordinary Differential Equations using Separable Integral-Matching #1850

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whedon opened this issue Oct 30, 2019 · 66 comments
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@whedon whedon commented Oct 30, 2019

Submitting author: @ramiyaari (Rami Yaari)
Repository: https://github.com/ramiyaari/simode/
Version: v1.1.8
Editor: @mjsottile
Reviewer: @cscherrer, @jgoldfar, @osorensen
Archive: 10.5281/zenodo.3576265

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/645cf34d694b5976179507afb8b7d61c"><img src="https://joss.theoj.org/papers/645cf34d694b5976179507afb8b7d61c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/645cf34d694b5976179507afb8b7d61c/status.svg)](https://joss.theoj.org/papers/645cf34d694b5976179507afb8b7d61c)

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

@cscherrer & @jgoldfar & @osorensen, 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 @mjsottile know.

Please try and complete your review in the next two weeks

Review checklist for @cscherrer

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

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 (@ramiyaari) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @jgoldfar

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

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 (@ramiyaari) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @osorensen

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

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 (@ramiyaari) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?
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@whedon whedon commented Oct 30, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @cscherrer, @jgoldfar, @osorensen it looks like you're currently assigned to review this paper 🎉.

⭐️ 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:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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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
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@whedon whedon commented Oct 30, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 30, 2019

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@cscherrer cscherrer commented Nov 11, 2019

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@osorensen osorensen commented Nov 28, 2019

@whedon generate pdf

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@whedon whedon commented Nov 28, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 28, 2019

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@ramiyaari ramiyaari commented Nov 30, 2019

@whedon generate pdf

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@whedon whedon commented Nov 30, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 30, 2019

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@mjsottile mjsottile commented Dec 2, 2019

It looks like we only have a couple boxes to check in the review checklists above. @cscherrer and @jgoldfar - can you take a look at the remaining items on your checklists to see if they have been addressed to your satisfaction?

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@jgoldfar jgoldfar commented Dec 3, 2019

Done

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@mjsottile mjsottile commented Dec 6, 2019

@ramiyaari it looks like the review checklists are complete. I will look everything over in a few days when I return from travel and see what the next steps are.

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@mjsottile mjsottile commented Dec 6, 2019

Can the reviewers @cscherrer, @jgoldfar, @osorensen confirm their recommendation to accept the submission by responding in this thread?

Also, @ramiyaari - I see that there is a pull request still waiting for a documentation correction. Can you address that and close the open pull request?

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@osorensen osorensen commented Dec 7, 2019

@mjsottile , I confirm my recommendation.

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@ramiyaari ramiyaari commented Dec 8, 2019

Thanks @mjsottile . I've merged the pull request.

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@jgoldfar jgoldfar commented Dec 9, 2019

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@cscherrer cscherrer commented Dec 9, 2019

Sorry I had missed this. Yes, I confirm my recommendation

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@mjsottile mjsottile commented Dec 13, 2019

@whedon generate pdf

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@whedon whedon commented Dec 13, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 19, 2019

OK. 10.5281/zenodo.3576265 is the archive.

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@mjsottile mjsottile commented Dec 19, 2019

@whedon set v1.1.8 as version

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@whedon whedon commented Dec 19, 2019

OK. v1.1.8 is the version.

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@mjsottile mjsottile commented Dec 19, 2019

Thanks @ramiyaari - I believe we're ready for final processing.

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@mjsottile mjsottile commented Dec 19, 2019

👋 @openjournals/joss-eics This paper has completed the review process and I believe it's ready for final processing. Let me know if there is anything additional that I should do.

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@ramiyaari ramiyaari commented Dec 19, 2019

Thank you @mjsottile

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@labarba labarba commented Dec 19, 2019

@ramiyaari — I'm the associate EiC on rotation, and will process your paper to publication. We ask authors to edit the metadata (in this case, the title) of the Zenodo deposit so it matches the JOSS paper. Could you make that change?

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@labarba labarba commented Dec 19, 2019

Looking at the paper, it does look rather long for the typical JOSS paper. In fact, the JOSS documentation stipulates that papers should be short: "The paper should be between 250-1000 words." And also,

a “full length” paper is not permitted, and software documentation such as API (Application Programming Interface) functionality should not be in the paper and instead should be outlined in the software documentation.

Do you think the detailed example should rather be in the documentation, and simply be mentioned here with a link?

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@ramiyaari ramiyaari commented Dec 22, 2019

@whedon generate pdf

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@whedon whedon commented Dec 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 22, 2019

PDF failed to compile for issue #1850 with the following error:

Can't find any papers to compile :-(

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@ramiyaari ramiyaari commented Dec 22, 2019

@whedon generate pdf

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@whedon whedon commented Dec 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 22, 2019

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@ramiyaari ramiyaari commented Dec 22, 2019

@whedon generate pdf

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@whedon whedon commented Dec 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 22, 2019

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@ramiyaari ramiyaari commented Dec 22, 2019

Hi @labarba, I've fixed the title of the Zenodo to match that of the JOSS paper.
I've also edited the paper and reduced the space taken by the example by two pages.
If that is still too long than I will remove the example completely,
but I was looking for example at this paper (https://joss.theoj.org/papers/10.21105/joss.01601)
and saw it is similar in length to what we have now.

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@labarba labarba commented Dec 22, 2019

@whedon accept

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@whedon whedon commented Dec 22, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Dec 22, 2019


OK DOIs

- 10.18637/jss.v033.i09 is OK
- 10.1155/2013/897658 is OK
- 10.1371/journal.pcbi.1004012 is OK
- 10.1098/rsif.2016.0525 is OK
- 10.1016/j.spl.2017.08.013 is OK
- 10.1177/0962280217746443 is OK
- 10.1111/stan.12124 is OK
- 10.18637/jss.v075.i02 is OK
- 10.1007/s11222-014-9486-9 is OK
- 10.1214/15-EJS1053 is OK
- 10.1111/biom.12348 is OK
- 10.1098/rsif.2010.0412 is OK
- 10.1016/j.jmva.2008.03.005 is OK
- 10.1111/j.1541-0420.2008.01172.x is OK
- 10.1093/bioinformatics/bth140 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Dec 22, 2019

Check final proof 👉 openjournals/joss-papers#1198

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1198, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@labarba labarba commented Dec 22, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Dec 22, 2019
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@whedon whedon commented Dec 22, 2019

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Dec 22, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Dec 22, 2019

🚨🚨🚨 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 👉 openjournals/joss-papers#1199
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01850
  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...

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@labarba labarba commented Dec 22, 2019

Congratulations, @ramiyaari, your JOSS paper is published! 🚀

Huge thanks to our editor: @mjsottile, and the reviewers: @cscherrer, @jgoldfar, @osorensen — we are so grateful for your contributions 🙏

@labarba labarba closed this Dec 22, 2019
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@whedon whedon commented Dec 22, 2019

🎉🎉🎉 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.01850/status.svg)](https://doi.org/10.21105/joss.01850)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01850">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01850/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01850/status.svg
   :target: https://doi.org/10.21105/joss.01850

This is how it will look in your documentation:

DOI

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