Joss-reviews: [REVIEW]: comorbidity: An R package for computing comorbidity scores

[whedon]

Submitting author: @ellessenne (Alessandro Gasparini)
Repository: https://github.com/ellessenne/comorbidity
Version: 0.1.0
Editor: @leeper
Reviewer: @corinne-riddell
Archive: 10.5281/zenodo.1209837

Status

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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

@corinne-riddell, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @leeper know.

Review checklist for @corinne-riddell

Conflict of interest

• [x] 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

• [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] Version: Does the release version given match the GitHub release (0.1.0)?
• [x] Authorship: Has the submitting author (@ellessenne) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] 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. @corinne-riddell it looks like you're currently assigned as the reviewer for this paper :tada:.

: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:

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

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[corinne-riddell]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

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# Compile the paper
@whedon generate pdf

[corinne-riddell]

Hi @ellessenne,

Nice package! I've learned a lot reading your code and it was interesting to read about the comorbidity scores based on ICD codes.

I've opened three issues with a few suggestions to improve documentation in the README, and return descriptions for the comorbidity function. I also have an issue regarding testthat, but it may be a misunderstanding on my end.

I have also left unchecked two items above to be addressed:

• please add community guidelines to your documentation
• there is also an item re: clear statement of dependencies. I didn't find any, but not sure of the protocol if your package doesn't have any.

Once these items are addressed we can loop in the editor and keep the ball rolling.

[leeper]

Thanks for your review, @corinne-riddell!!

@ellessenne Once you've had a chance to respond to these points and the open issues, please leave me a message here and I will give everything a final check.

[ellessenne]

Thank you very much @corinne-riddell for your review!
I merged your pull requests and I am going to work on the issues you raised straight away. Very helpful!
Regarding the two unchecked items left to be addressed:
1- I can add a CONTRIBUTING.md file to the repository;
2- I can add explicit dependencies on the README file, it would be the same packages included in the
DESCRIPTION file.
@leeper, would this be ok?
Thanks!

[leeper]

No need to list dependencies beyond the DESCRIPTION file. I'll tick that one for you.

[ellessenne]

Thanks @leeper; I also just added contributing guidelines and code of conduct to the repository.

@corinne-riddell, I made some changes following your PRs / Issues, could you please give it a check? Thank you!

[corinne-riddell]

@ellessenne @leeper looks great, I think we're good to go on accepting this. Good job @ellessenne 👍

[leeper]

Excellent. Thanks, @corinne-riddell!!

[leeper]

@ellessenne Can you please generate an archive of your repository using, for example, figshare or zenodo and then include the DOI for the archive in a comment here? Once I have that, we can accept your paper in JOSS!

[ellessenne]

Thank you very much again @corinne-riddell and @leeper!
I uploaded the current version of comorbidity to Zenodo, the corresponding DOI is: 10.5281/zenodo.1209837. I think the link (via doi.org) is not active yet, I am not sure how long it will take but should be ok!

[leeper]

@whedon set 10.5281/zenodo.1209837 as archive

[whedon]

OK. 10.5281/zenodo.1209837 is the archive.

[leeper]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[leeper]

@ellessenne Great. Thank you! We should be all set.

Thank you, again, @corinne-riddell!! Hope you enjoyed your first review for JOSS!

@arfon Over to you.

[ellessenne]

Thank you all! This was a great experience overall, and I would like to contribute to the project - @leeper, if you need reviewers for R / epidemiology / biostatistics manuscripts please don't hesitate to contact me!

[leeper]

@ellessenne Glad to hear it was a good experience! Please sign-up to be a reviewer here: http://joss.theoj.org/reviewer-signup.html

[arfon]

@corinne-riddell - many thanks for your review here and to @leeper for editing this submission ✨

@ellessenne - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00648 ⚡️:rocket: :boom:

[whedon]

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

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This is how it will look in your documentation:

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