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[REVIEW]: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software #978

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whedon opened this Issue Sep 25, 2018 · 19 comments

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whedon commented Sep 25, 2018

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

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/ccb887b4991abca9517847b016cdb33d"><img src="http://joss.theoj.org/papers/ccb887b4991abca9517847b016cdb33d/status.svg"></a>
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

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

Review checklist for @strengejacke

Conflict of interest

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 (0.2.1 (development version; most recent CRAN version is 0.2.0))?
  • Authorship: Has the submitting author (@jrosen48) 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)?
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whedon Sep 25, 2018

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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 🎉.

⭐️ 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:

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

watching

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

notifications

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

@whedon commands
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whedon commented Sep 25, 2018

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 🎉.

⭐️ 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:

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

watching

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

notifications

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

@whedon commands
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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Sep 25, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Sep 25, 2018

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strengejacke Oct 2, 2018

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

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strengejacke commented Oct 2, 2018

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

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arfon Oct 2, 2018

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

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arfon commented Oct 2, 2018

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

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jnese Oct 2, 2018

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

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jnese commented Oct 2, 2018

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

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

Ideally in the next couple of weeks?

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arfon commented Oct 2, 2018

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

Ideally in the next couple of weeks?

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jnese Oct 2, 2018

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

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jnese commented Oct 2, 2018

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

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jnese Oct 9, 2018

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Ok, my review is complete.

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jnese commented Oct 9, 2018

Ok, my review is complete.

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

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arfon commented Oct 9, 2018

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

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jnese Oct 9, 2018

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

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jnese commented Oct 9, 2018

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

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strengejacke Oct 10, 2018

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Yes, accept from my point of view.

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strengejacke commented Oct 10, 2018

Yes, accept from my point of view.

@arfon arfon added the accepted label Oct 10, 2018

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@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.

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arfon commented Oct 10, 2018

@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.

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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.

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jrosen48 commented Oct 10, 2018

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.

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

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jrosen48 commented Oct 10, 2018

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

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@whedon set 10.5281/zenodo.1455773 as archive

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arfon commented Oct 10, 2018

@whedon set 10.5281/zenodo.1455773 as archive

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OK. 10.5281/zenodo.1455773 is the archive.

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whedon commented Oct 10, 2018

OK. 10.5281/zenodo.1455773 is the archive.

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@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 ⚡️ 🚀 💥

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arfon commented Oct 10, 2018

@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 ⚡️ 🚀 💥

@arfon arfon closed this Oct 10, 2018

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

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

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.00978/status.svg)](https://doi.org/10.21105/joss.00978)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00978">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00978/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00978/status.svg
   :target: https://doi.org/10.21105/joss.00978

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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whedon commented Oct 10, 2018

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

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

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.00978/status.svg)](https://doi.org/10.21105/joss.00978)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00978">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00978/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00978/status.svg
   :target: https://doi.org/10.21105/joss.00978

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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