[REVIEW]: cleanEHR: The critical care EHR analysis tools

[whedon]

Submitting author: @sinanshi (Sinan Shi)
Repository: https://github.com/ropensci/cleanEHR
Version: v1.0
Editor: @arfon
Reviewer: @arfon
Archive: 10.5281/zenodo.1117244

Status

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Markdown: [![status](https://joss.theoj.org/papers/4cb8b3f995b60521c2019cc8d87fc1c0/status.svg)](https://joss.theoj.org/papers/4cb8b3f995b60521c2019cc8d87fc1c0)

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) 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

@arfon, 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
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Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Version: Does the release version given match the GitHub release (v0.1.0)?
• Authorship: Has the submitting author (@sinanshi) 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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @arfon it looks like you're currently assigned as the reviewer for 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:

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For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #513 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse': (tmp/513/paper.md): found character that cannot start any token while scanning for the next token at line 4 column 1 (Psych::SyntaxError)
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse_stream'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in `parse'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:in `load'
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[arfon]

@whedon set 10.5281/zenodo.1117244 as archive

[whedon]

OK. 10.5281/zenodo.1117244 is the archive.

[arfon]

Accepting because of submission to rOpenSci: ropensci/software-review#102

[arfon]

@sinanshi - I've fixed up some issues with your paper.md here ropensci-archive/cleanEHR#151 .

Also, since you submitted originally, our submission guidelines have been updated a fair bit. Please take a look at the section 'What should my paper contain?' here http:https://joss.theoj.org/about#paper_structure

Finally, it looks like you're missing a bibliography. Please make sure you cite related work using the standard RMarkdown way: can read how to do that here)

[sinanshi]

Thanks @arfon, could you have a look if it is all OK now.

[arfon]

Thanks @sinanshi - I still think this paper could do with a little more detail. From the text of your paper it's still not very clear to me what this software does! Please consider adding just a little more prose, perhaps with an example use case to address this:

• A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience

Also, if there are any research projects using this software then please describe them too:

• Mentions (if applicable) of any ongoing research projects using the software or recent scholarly publications enabled by it

[sinanshi]

Thank you @arfon for your suggestions. I have updated the paper, adding the high-level functionality description. Regarding other related research project, there is no published research result so far using this package, despite many at the early stage of their research.

[arfon]

@sinanshi - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00513 ⚡️ 🚀 💥

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippet:

[![DOI](http:https://joss.theoj.org/papers/10.21105/joss.00513/status.svg)](https://doi.org/10.21105/joss.00513)

This is how it will look in your documentation:

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