Joss-reviews: [REVIEW]: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software

[whedon]

Submitting author: @jrosen48 (Joshua Rosenberg)
Repository: https://github.com/jrosen48/tidyLPA
Version: 0.2.1 (development version; most recent CRAN version is 0.2.0)
Editor: @arfon
Reviewer: @jnese, @strengejacke
Archive: 10.5281/zenodo.1455773

Status

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Markdown: [![status](http://joss.theoj.org/papers/ccb887b4991abca9517847b016cdb33d/status.svg)](http://joss.theoj.org/papers/ccb887b4991abca9517847b016cdb33d)

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

@jnese & @strengejacke, 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 @arfon know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @jnese

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 (0.2.1 (development version; most recent CRAN version is 0.2.0))?
• [x] Authorship: Has the submitting author (@jrosen48) 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)?

Review checklist for @strengejacke

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 (0.2.1 (development version; most recent CRAN version is 0.2.0))?
• [x] Authorship: Has the submitting author (@jrosen48) 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, a robot that can help you with some common editorial tasks. @jnese, 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]

:point_right: Check article proof :page_facing_up: :point_left:

[strengejacke]

Ok, from my side all issues have been addressed adequately, so I have no further requests to the author(s).

[arfon]

@jnese - how are you getting along with your review?

[jnese]

It is coming along. Do you have a date by which you would like it completed?

[arfon]

It is coming along. Do you have a date by which you would like it completed?

Ideally in the next couple of weeks?

[jnese]

Absolutely. I hope to have it completed in less time than that.

[jnese]

Ok, my review is complete.

[arfon]

Thanks @jnese, @strengejacke! Can I check that you are both happy to accept this submission at this point?

[jnese]

I am happy to accept at this time. Thank you.

[strengejacke]

Yes, accept from my point of view.

[arfon]

@jrosen48 - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[jrosen48]

Thank you @strengejacke and @jnese for lending your time and expertise - the package is better and I appreciate the feedback you provided in terms of revisions to make after the paper is accepted, too! Thank you @arfon for your work on this, too - this was a helpful and illuminating peer-review experience and I appreciate your time and expertise as well.

[jrosen48]

@arfon thank you again! The archive (on Zenodo) is here: https://zenodo.org/record/1455773#.W745vFIpAW8 and the doi is 10.5281/zenodo.1455773

[arfon]

@whedon set 10.5281/zenodo.1455773 as archive

[whedon]

OK. 10.5281/zenodo.1455773 is the archive.

[arfon]

@jnese, @strengejacke - many thanks for your reviews here ✨

@jrosen48 - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00978 :zap: :rocket: :boom:

[whedon]

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

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reStructuredText:
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[jrosen48]

@arfon per our conversation via e-mail about adding an acknowledgment, I've added an Acknowledgment section to the paper with the following text:

This material is based upon work supported by the National Science Foundation under Grant No. 1661064. Any opinions, findings, conclusions, or recommendations expressed in this material are those of the authors and do not reflect the views of the National Science Foundation.

Can we please update the paper with this one addition?

[arfon]

@jrosen48 - that's updated now. Please note that the PDF can take a while to show as updated on the JOSS site due to caching.

[jrosen48]

Thanks so much @arfon