Joss-reviews: [REVIEW]: Extracting, Computing and Exploring the Parameters of Statistical Models using R

Created on 6 Jul 2020  ·  76Comments  ·  Source: openjournals/joss-reviews

Submitting author: @strengejacke (Daniel Lüdecke)
Repository: https://github.com/easystats/parameters
Version: 0.8.3
Editor: @sbenthall
Reviewers: @cmaimone, @Ohlsen
Archive: 10.5281/zenodo.4004846

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Status

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Markdown: [![status](https://joss.theoj.org/papers/158e1c7d5be57a0a70f137ca6cbf6912/status.svg)](https://joss.theoj.org/papers/158e1c7d5be57a0a70f137ca6cbf6912)

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

@cmaimone, 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 @sbenthall know.

Please try and complete your review in the next six weeks

Review checklist for @cmaimone

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

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

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: Do the authors clearly state 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 @Ohlsen

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

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

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: Do the authors clearly state 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?
accepted published recommend-accept review

Most helpful comment

My review is complete. Recommend accept.

All 76 comments

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @cmaimone 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.

:star: Important :star:

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

notifications

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
Reference check summary:

OK DOIs

- 10.21105/joss.01541 is OK
- 10.21105/joss.01412 is OK
- 10.18637/jss.v016.i09 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@sbenthall Do you know why @Ohlsen has been unassigned as reviewer?

@strengejacke I don't. Let me ask ... @juanjo any idea what happened here?

@whedon generate pdf

@cmaimone Dear Christina, thank you for your reviews regarding our package (website) and the paper. We have addressed your issues and included a response to your requests in the related GitHub issues (https://github.com/easystats/parameters/issues/274, https://github.com/easystats/parameters/issues/276 and https://github.com/easystats/parameters/issues/277).

We hope that our revisions adequately address your proposed changes. Please let us know if there are any further things you like us to revise.

@whedon generate pdf

We did some language revisions to the paper as well now.

@whedon generate pdf

We created Zenodo-repositories to assign our packages with a DOI, so all references should have a DOI now (where possible).

My review is complete. Recommend accept.

@whedon generate pdf

@sbenthall I have made all corrections to the paper and also checked correct spelling/upper-lower-case in references - all should be fine now. What would be the next step?

@whedon assign Ohlsen as reviewer

OK, Ohlsen is now a reviewer

Hmm. That didn't work. I'm trying to reassign @Ohlsen . Sorry, I'm new here.

@whedon add @cmaimone as reviewer

OK, @cmaimone is now a reviewer

@whedon add @Ohlsen as reviewer

OK, @Ohlsen is now a reviewer

Ok, I think maybe @Ohlsen did something manually that unassigned them.
But now I've reassigned them. I believe they need to complete their review in addition to @cmaimone in order to proceed.

@xuanxu please let me know if that doesn't look right for some reason.

@sbenthall I've added manually the review checklist for @Ohlsen in the body of the issue. Everything looks ok now.

Thanks!

@sbenthall @Ohlsen After revising the paper and package based on the first review, CRAN requested an update from the _parameters_ package. Thus, I needed to increase the version number to indicate a "stable" release, and the GitHub-version will be 0.8.2.x the next days, and no longer 0.8.1.x - so don't be confused, @Ohlsen , when you start your review.

This is still waiting on @Ohlsen for review

Hi, @sbenthall, apparently i missed some notification and am also not able to edit the checklist. Could you start the invitation again? Sorry for the trouble my self-assignment caused. I´m new to this as well ...

@whedon commands

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

I´m still not able to edit the checklist. I tried the steps suggested above:

Make sure you're logged in to your GitHub account

I am correctly logged in and also tried it in another browser with deleted cookies.

Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

Here, i get a red banner that my invitation can´t be found. Perhaps it might work if i´m re-invited and not only re-assigned?

@xuanxu Do you have a guess, why @Ohlsen cannot edit the review-checkboxes?

Maybe the invitation expired? Let's try to re-invite

@whedon re-invite @Ohlsen as reviewer

OK, the reviewer has been re-invited.

@ohlsen please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

Is it working now @Ohlsen ?

@sbenthall Yes! Thank you, i´ll review now

I finished my review, too. I had some feature requests focusing in particular on the packages functionality towards lavaan-models, which are already solved . I recommend accept as well.

Thanks, @Ohlsen, for your suggestions. Regarding your issues:

1) We revised the output for structural equation models, so model_parameters() now also include self-defined parameters (https://github.com/easystats/parameters/issues/290).
2) Since the vignettes on model_parameters() for the _lavaan_ package only focussed on CFA, we also added a small example for SEM as well.
3) We fixed some typos found in the paper.
4) To improve support for structural equation models, we revised model_parameters() so it can include different types of standardized solutions (https://github.com/easystats/parameters/issues/291).

We hope we adequately addressed all issues!

Thank you, reviewers.

@strengejacke , as a next step, would you please :

  • issue a new tagged release of the software (if changed),
  • archive it (on Zenodo, figshare, or other).
  • post the version number and archive DOI in this REVIEW issue.

Thank you @sbenthall

@sbenthall I have finished all requested steps, I think. Can you confirm that no further action from my side is required at the moment?

@whedon generate pdf

@whedon check references

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

OK DOIs

- 10.21105/joss.01541 is OK
- 10.21105/joss.01412 is OK
- 10.18637/jss.v016.i09 is OK
- 10.1177/2515245918770963 is OK
- 10.5281/zenodo.3952174 is OK
- 10.5281/zenodo.3952153 is OK
- 10.5281/zenodo.3952214 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon set 10.5281/zenodo.4004846 as archive

OK. 10.5281/zenodo.4004846 is the archive.

@whedon set 0.8.3 as version

OK. 0.8.3 is the version.

This paper is ready to be accepted.

Before I do so finally, may I ask you @strengejacke to please check the proof one last time?

This is for your full satisfaction with the article, as making changes after the acceptance is more difficult.

Thank you, @sbenthall. I carefully proof-read the paper. Everything is fine for me, I'm ok with publication.

@sbenthall - it looks like this is ready for you to @whedon accept and then I can take it, do a final proofread, and then publish it

@whedon accept

Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01541 is OK
- 10.21105/joss.01412 is OK
- 10.18637/jss.v016.i09 is OK
- 10.1177/2515245918770963 is OK
- 10.5281/zenodo.3952174 is OK
- 10.5281/zenodo.3952153 is OK
- 10.5281/zenodo.3952214 is OK

MISSING DOIs

- None

INVALID DOIs

- None

: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/1721

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1721, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

Your submission is accepted, @strengejacke

Thank you for your article!

Thanks for editing this publication!

Your submission is accepted, @strengejacke

Thank you for your article!

@sbenthall - FYI, this is not accepted, it's "recommended for acceptance". See the label...

Accepted happens when it is published, which I hope will happen soon :)

@strengejacke - please update the metadata in the Zenodo archive so that the title matches the paper title.

Also, for the Saefken reference, please add the URL to the arxiv abstract

Once these are done, I will finalize the acceptance and publication

@whedon generate pdf

I revised the title of the Zenodo archive and added the URL. Generating PDF again to check if URL is fine...

Yes, URL is ok!

@whedon accept deposit=true

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

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

🚨🚨🚨 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/1722
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02445
  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...

Congratulations to @strengejacke (Daniel Lüdecke) and co-authors!!

Thanks to @cmaimone & @Ohlsen for reviewing, and @sbenthall for editing!

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

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HTML:
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reStructuredText:
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This is how it will look in your documentation:

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