[REVIEW]: medrxivr: Accessing and searching medRxiv and bioRxiv preprint data in R

[whedon]

Submitting author: @mcguinlu (Luke A McGuinness)
Repository: https://github.com/ropensci/medrxivr
Version: v0.0.3
Editor: @danielskatz
Reviewer: @danielskatz
Archive: 10.5281/zenodo.3860023

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Review checklist for @danielskatz

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.

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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 (@mcguinlu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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?

[whedon]

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 🎉.

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[whedon]

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

OK DOIs

- 10.22541/au.158516578.89167184 is OK
- 10.1136/bmj.l2301 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[arfon]

👋 @mcguinlu - thanks for your submission to JOSS. Unfortunately, even though this submission came via rOpenSci, this submission is out of scope for JOSS as we classify it a 'minor' submission (API wrapper). I've asked the rOpenSci folks to update their guidelines to make it a little clearer which rOpenSci packages might be considered out of scope here.

/ cc @karthik

[arfon]

@whedon reject

[whedon]

Paper rejected.

[mcguinlu]

Hi @arfon,

Thanks for your comments, though I'll admit I am a little surprised that the package is not considered in scope.

While medrxivr does interact with the API, this is mainly as a precusor to searching the medRxiv database using complex search strategies and then bulk exporting the results to a .BIB file for further processing/analysis as part of a systematic literaure review. This functionality (reproducible + transparent searching, bulk export of records) is something that is not offered by either the medRxiv website or its API, or by any other package/tool, but is regularly requested by the health librarian community:

I have pretty much given up on medRxiv, it search interface is useless & unpredictable. I have many searches that I have rerun exactly the same week prior that have come back with inconsistent wacky results. No way should a search one week get 60 citations then 3000 next #medlibs

— Michelle Kraft (@krafty) August 13, 2020

anyone have a method for bulk export from medRxiv? #systematicreviews #rapidreviews #ukmedlibs #medlibs #thanks

— (((MarshallDozier))) (@mafrado) March 31, 2020

Re-amplifying this question. I'm grappling with medRxiv this morning and having issues downloading. Any ideas #medlibs people? https://t.co/pBB8j7hy8U

— Jane Falconer (@falkie71) April 24, 2020

In addition, the main functionality of the package was developed before the medRxiv API came online - previously medrxivr used webscraping to import the data (for example, see this commit point from back in February), which is why I think the designation as an "API wrapper" might not be accurate.

Finally, just to make you aware that the package has already been used in two published academic publications that I know of (see here and here) (COI: I am one of the co-authors on the second paper)

I fully respect your decision as EiC, but just wanted to make sure that the decision wasn't due to an error on my part, in that I may not have accurately described medrxivr in the paper I submitted.

Thanks for your continued consideration!

---

Edit: I went looking out of interest, and just in case it helps, I would consider medrxivr to be comparable to the JOSS-published chirps package, in that it provides access to the data via the API but also contains functions to work with the data once imported.

[mcguinlu]

Good morning @arfon (& @danielskatz, for reference ), and happy Monday!

As it's been a week, just flagging the above again in case it got lost in the mix - would be great to hear what you think, particularly re: comparison with chirps.

[danielskatz]

@mcguinlu asked me to reopen this so that he could further discuss it with @arfon and the JOSS team, so I am doing so

[mcguinlu]

Thanks @danielskatz!

Also just flagging this to @maelle, as I know she has done a lot of work recently on updating the rOpenSci dev guide, and I agree with @arfon's point above that it might be useful to have clear guidelines on the types of rOpenSci packages that are considered out of scope by JOSS included in the rOpenSci dev guide.

[karthik]

Thanks @mcguinlu. We have started a discussion to update the dev guide so it clearly reflects what might be out of scope for JOSS.

[danielskatz]

@mcguinlu - we're going to process this in JOSS.

[danielskatz]

This package has been reviewed by rOpenSci: ropensci/software-review#380

[danielskatz]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[danielskatz]

@whedon check references

[whedon]

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

OK DOIs

- 10.22541/au.158516578.89167184 is OK
- 10.1136/bmj.l2301 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@mcguinlu - can you merge ropensci/medrxivr#12 or let me know what part of it you disagree with?

[danielskatz]

Also, is this code in zenodo or another archive? If so, what is the DOI for it there? In ropensci/software-review#380 (comment) it looks like that item is checked off...

[mcguinlu]

Hi @danielskatz,

I've merged the changes you made in ropensci/medrxivr#12 into the main branch now. And the code for this package is archived by Zenodo. The Zenodo DOI is 10.5281/zenodo.3860023

[danielskatz]

@whedon set 10.5281/zenodo.3860023 as archive

[whedon]

OK. 10.5281/zenodo.3860023 is the archive.

[danielskatz]

In the zenodo archive, can you change the metadata so that the title and authors match those of the JOSS paper?

[mcguinlu]

Done - title and authors are now consistent between the JOSS paper and the Zenodo repo.

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.22541/au.158516578.89167184 is OK
- 10.1136/bmj.l2301 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1788

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1788, 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]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02651 joss-papers#1789
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02651
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations @mcguinlu!!

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[mcguinlu]

Awesome - thanks to everyone involved! 🥳