[REVIEW]: excluder: An R package that checks for exclusion criteria in online data

whedon commented 2 years ago

Submitting author: @JeffreyRStevens (Jeffrey R Stevens) Repository: https://github.com/ropensci/excluder/ Version: 0.3.1 Editor: @danielskatz Reviewer: @danielskatz Archive: 10.5281/zenodo.5648202

:warning: JOSS reduced service mode :warning:

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Status

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HTML: <a href="https://joss.theoj.org/papers/25a045841e7e91fdc25745cc458a1fd6"><img src="https://joss.theoj.org/papers/25a045841e7e91fdc25745cc458a1fd6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/25a045841e7e91fdc25745cc458a1fd6/status.svg)](https://joss.theoj.org/papers/25a045841e7e91fdc25745cc458a1fd6)

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Review checklist for @danielskatz

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@JeffreyRStevens) 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] 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?

whedon commented 2 years ago

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

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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@whedon commands

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

@whedon generate pdf

whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (980.4 files/s, 158245.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            30           1452            386           5253
R                               27            296           1419           2071
Markdown                         6            211              0            849
CSS                              3             99             48            428
JSON                             1              0              0            303
JavaScript                       3             64             32            256
SVG                              9              0              1            179
YAML                             5             26              2            142
Rmd                              2             86            177            101
-------------------------------------------------------------------------------
SUM:                            86           2234           2065           9582
-------------------------------------------------------------------------------

Statistical information for the repository '87f56c1b78dbe0011121c352' was
gathered on 2021/11/05.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jeffrey Stevens                  1           352              0          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Jeffrey R. Stevens          352          100.0         -0.0                9.09

whedon commented 2 years ago

PDF failed to compile for issue #3893 with the following error:

 Can't find any papers to compile :-(

danielskatz commented 2 years ago

Accepted by rOpenSci in https://github.com/ropensci/software-review/issues/455

danielskatz commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

danielskatz commented 2 years ago

@whedon check references from branch paper

whedon commented 2 years ago

Attempting to check references... from custom branch paper

whedon commented 2 years ago

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

OK DOIs

- 10.1080/13645579.2018.1563966 is OK
- 10.1177/1948550619875149 is OK
- 10.3758/s13428-021-01694-3 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@JeffreyRStevens - is there already an archived version of this software in zenodo or a similar archival repository as part of the rOpenSci review? If so, what's the DOI and version of the software that was archived?

JeffreyRStevens commented 2 years ago

@danielskatz, no, not to my knowledge. Should I do that now?

danielskatz commented 2 years ago

Yes - the paper looks good to me, so the next steps are:

[ ] Make a tagged release of your software if needed, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

JeffreyRStevens commented 2 years ago

I have tagged the submitted version 0.3.1 on GitHub.
I have archived the software on Zenodo at https://doi.org/10.5281/zenodo.5648202 with the DOI of 10.5281/zenodo.5648202.

Was that everything?

danielskatz commented 2 years ago

Yes, that's it - I'll continue the process

danielskatz commented 2 years ago

@whedon set 0.3.1 as version

whedon commented 2 years ago

OK. 0.3.1 is the version.

danielskatz commented 2 years ago

@whedon set 10.5281/zenodo.5648202 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5648202 is the archive.

danielskatz commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

PDF failed to compile for issue #3893 with the following error:

 Can't find any papers to compile :-(

danielskatz commented 2 years ago

@whedon recommend-accept from branch paper

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

- 10.1080/13645579.2018.1563966 is OK
- 10.1177/1948550619875149 is OK
- 10.3758/s13428-021-01694-3 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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/2730

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2730, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch paper

danielskatz commented 2 years ago

@whedon accept deposit=true from branch paper

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/2731
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03893
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 @JeffreyRStevens (Jeffrey R Stevens) - your paper has now been accepted and published by JOSS!!

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.03893/status.svg)](https://doi.org/10.21105/joss.03893)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03893">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03893/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03893/status.svg
   :target: https://doi.org/10.21105/joss.03893

This is how it will look in your documentation:

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JeffreyRStevens commented 2 years ago

Many thanks, @danielskatz!

JeffreyRStevens commented 2 years ago

@danielskatz, I assume that I can remove the paper branch now?

danielskatz commented 2 years ago

Yes, that's fine

openjournals / joss-reviews