[REVIEW]: profileR: An R package for profile analysis

whedon commented 4 years ago

Submitting author: @cddesja (Christopher Desjardins) Repository: https://github.com/cddesja/profileR Version: v0.3-6 Editor: @marcosvital Reviewers: @wjakethompson, @jrosen48 Archive: 10.5281/zenodo.3711046

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/85980d724b2b7fc7d10f7fca27fbce92"><img src="https://joss.theoj.org/papers/85980d724b2b7fc7d10f7fca27fbce92/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/85980d724b2b7fc7d10f7fca27fbce92/status.svg)](https://joss.theoj.org/papers/85980d724b2b7fc7d10f7fca27fbce92)

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) by leaving comments 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

@wjakethompson & @jrosen48 & @markhwhiteii , please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @marcosvital know.

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

Review checklist for @wjakethompson

Conflict of interest

[x] 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.

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] Contribution and authorship: Has the submitting author (@cddesja) 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

Review checklist for @jrosen48

Conflict of interest

[x] 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.

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] Contribution and authorship: Has the submitting author (@cddesja) 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).
[ ] 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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

Review checklist for @markhwhiteii

Conflict of interest

[x] 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.

Code of Conduct

[x] 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?
[ ] Contribution and authorship: Has the submitting author (@cddesja) 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 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 commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @wjakethompson, @jrosen48, @markhwhiteii it looks like you're currently assigned to review 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:

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

watching

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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon commented 4 years ago

Attempting to check references...

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago


OK DOIs

- 10.1037//1082-989X.7.4.468 is OK

MISSING DOIs

- https://doi.org/10.1080/00273170903187665 may be missing for title: Factor Analytic Modeling of Within Person Variation in Score Profiles
- https://doi.org/10.1201/b20498 may be missing for title: Handbook of educational measurement and psychometrics using R

INVALID DOIs

- None

whedon commented 4 years ago

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

jrosen48 commented 4 years ago

Hi, sorry for my delay on this. I will aim to proceed with my review this week.

cddesja commented 4 years ago

Is there an update on the timeline for the review?

marcosvital commented 4 years ago

Hi, everyone!

@cddesja , sorry about the delayed reply, I'm still organizing myself after a few weeks out of office.

@wjakethompson , @jrosen48 and @markhwhiteii, let us know when you have the time to look into this review, ok? And please feel free to contact me if you have any questions about the reviewing process.

Best regards

Marcos

jrosen48 commented 4 years ago

Hi @marcosvital, I seem to be unable to check the checkbox items - can you advise if there is something I can do? thanks!

kthyng commented 4 years ago

Hi @jrosen48 — did you receive an invitation to edit by email? You need to accept that to gain proper permissions on this issue. Let me know if you don't have the invitation.

jrosen48 commented 4 years ago

Hi, I checked my email, but didn't see this! Is there any chance that you would be able to invite me again? Thank you!

kthyng commented 4 years ago

@jrosen48 hm, check out the list up above under "Reviewer instructions & questions" and see if you have done both those things (being logged into github and it gives a page for invites).

jrosen48 commented 4 years ago

doh, so sorry - thanks - that did it. I'm sorry!

wjakethompson commented 4 years ago

I have completed my initial review. Overall, it looks like great package! A summary of why some boxes have not been checked:

Acceptance blockers

Example usage: See cddesja/profileR#28.
Automated tests: See cddesja/profileR#29.
Community guidelines: See cddesja/profileR#30.

Other issues

License: A license is included, conflicts with the license listed in the DESCRIPTION. See cddesja/profileR#32.
Installation instructions: Instructions are included, and work. But I think CRAN instructions should also be included. See cddesja/profileR#27.
State of the field: No comparisons are made to other packages. See cddesja/profileR#31.
References: Assuming packages are added for state of the field, appropriate references would also need to be included.

cddesja commented 4 years ago

@jrosen48 and @wjakethompson, I believe we have addressed all the outstanding issues. @jrosen48, please let us know if you think the state of the field has been described adequately.

cddesja commented 4 years ago

@wjakethompson, we are wondering if the changes we've made are adequate for you and whether you have any additional changes?

@kthyng, we haven't heard back from @markhwhiteii. should we try and get another reviewer or if both @wjakethompson and @jrosen48 are satisfied with the state of the paper, is that sufficient?

wjakethompson commented 4 years ago

@cddesja Everything looks good to me!

kthyng commented 4 years ago

@cddesja Let's check with @marcosvital, who is the handling editor.

@marcosvital Did you want to have 3 reviewers for this submission in particular or are you ok with two?

marcosvital commented 4 years ago

Hi, @kthyng , yes, I'm comfortable with moving on with two reviews, as they are both satisfied with the paper.

@wjakethompson ad @jrosen48 , thank you both so much for taking time to review and make suggestions. @jrosen48, I noticed that there is one last box left unchecked in you review, regarding "Functionality documentation". Do you fell there is still something concerning this that the authors should address?

@cddesja , we are almost done here. Once we confirm that everything is ok to move forward, you will need to archive the last release of the package (on Zenodo, figshare, or other), if you already didn't do this, post the version number and archive DOI here in this issue.

cddesja commented 4 years ago

@marcosvital, sounds good. Are you waiting on me, right now? Or are we waiting on

@jrosen48, I noticed that there is one last box left unchecked in you review, regarding "Functionality documentation". Do you fell there is still something concerning this that the authors should address?

marcosvital commented 4 years ago

Hi, @cddesja! I was waiting to know about the unchecked box. But since it's just a single item from the whole list, I'll make a final and quick check on everything myself, and we'll move on, ok? Will be back here soon.

marcosvital commented 4 years ago

Hello again, @cddesja, I think that everything seems ok, so let's proceed with our last steps towards acceptance!

marcosvital commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

marcosvital commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1037//1082-989X.7.4.468 is OK

MISSING DOIs

- https://doi.org/10.1080/00273170903187665 may be missing for title: Factor Analytic Modeling of Within Person Variation in Score Profiles
- https://doi.org/10.1201/b20498 may be missing for title: Handbook of educational measurement and psychometrics using R
- https://doi.org/10.21105/joss.00978 may be missing for title: tidyLPA: An R package to easily carry out Latent Profile Analysis (LPA) using open-source or commercial software
- https://doi.org/10.32614/rj-2016-021 may be missing for title: mclust 5: clustering, classification and density estimation using Gaussian finite mixture models

INVALID DOIs

- None

marcosvital commented 4 years ago

@cddesja, please check out the manuscript references: they should have the DOIs listed, ok?

marcosvital commented 4 years ago

@markhwhiteii, as JOSS requires only two reviewers, we are proceeding with the paper acceptance. Since the reviewers are listed on the published paper, I'll remove your name from the list. I understand that taking time to review a paper is not easy, so thanks for trying to help with this one, and I hope we can count on you in future reviewing tasks.

marcosvital commented 4 years ago

@whedon remove @markhwhiteii as reviewer

whedon commented 4 years ago

OK, @markhwhiteii is no longer a reviewer

okanbulut commented 4 years ago

@cddesja, please check out the manuscript references: they should have the DOIs listed, ok?

@marcosvital, I fixed the missing DOIs in the paper. They all should be good now. Thank for catching that. We can probably re-combile the PDF and check it once more.

cddesja commented 4 years ago

@marcosvital, I'd like to make a reference to our two vignettes included in the package by adding the following sentence bolded below. Is this okay? I'll add the citation to the paper.bib if this is fine.

The R package profileR, currently in version 0.3-6 on the comprehensive R archive network (CRAN), implements profile reliability [@bulut2013between; @bulut2017], criterion-related profile analysis [@davison_identifying_2002], profile analysis via multidimensional scaling [@pams], moderated profile analysis, profile analysis by group, and a within-person factor model to derive score profiles [@davison2009factor] as well as a variety of graphical methods to visualize profiles. Related profile analysis packages exist in R, such as tidyLPA [@rosenberg2019tidylpa] and mclust [@mclust], as well as in Mplus [@muthen2004mplus], however, our approach does not rely on mixture modeling and aims to provide access to a wider range of profile analytic techniques. An extensive vignette documenting profileR [@bulut2020] is included with the package as well as vignette to ensure the functionality of the package locally.

If this is fine with you, then I'll add this to the paper.md and bib file then I'll archive the package on Zendodo.

arfon commented 4 years ago

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

cddesja commented 4 years ago

@arfon, the paper is done. I posted the software on Zendodo. DOI: 10.5281/zenodo.3711046 Version: 0.3-6 The paper.md and paper.bib files are done.

arfon commented 4 years ago

👍 roger that @cddesja. We'll just wait to hear back from @marcosvital before finalizing the accept/publish steps.

marcosvital commented 4 years ago

Everything looks fine, so we can move on to acceptance! Let's make a final check on references and proof.

marcosvital commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1037//1082-989X.7.4.468 is OK
- 10.1080/00273171.2016.1253452 is OK
- 10.1080/00273170903187665 is OK
- 10.1201/b20498 is OK
- 10.21105/joss.00978 is OK
- 10.32614/rj-2016-021 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.31234/osf.io/sgy8m is INVALID because of 'https://doi.org/' prefix

marcosvital commented 4 years ago

@cddesja , there is a final invalid DOI. Can you check and correct it?

okanbulut commented 4 years ago

@cddesja @marcosvital , the invalid DOI has been fixed now. Thanks!

cddesja commented 4 years ago

Can I look at the final proof just to make it looks okay? Thanks for fixing the DOI, Okan. Chris

On Mar 16, 2020, at 9:33 AM, Okan Bulut notifications@github.com wrote:

@cddesja @marcosvital , the invalid DOI has been fixed now. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

marcosvital commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1037//1082-989X.7.4.468 is OK
- 10.1080/00273171.2016.1253452 is OK
- 10.1080/00273170903187665 is OK
- 10.1201/b20498 is OK
- 10.21105/joss.00978 is OK
- 10.31234/osf.io/sgy8m is OK
- 10.32614/rj-2016-021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

marcosvital commented 4 years ago

Thank you for correcting it, @okanbulut , everything seems fine!

@cddesja , I'll generate another proof.

marcosvital commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

cddesja commented 4 years ago

Okay, I changed profileR to profileR and uploaded the new paper.md. Everything else looks good to me.

On Mon, Mar 16, 2020 at 10:22 AM whedon notifications@github.com wrote:

👉 Check article proof 📄 👈 https://github.com/openjournals/joss-papers/blob/joss.01941/joss.01941/10.21105.joss.01941.pdf

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1941#issuecomment-599563335, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAMIZ2YSSVTHREFLRV6LL73RHYYZJANCNFSM4JZCQC7A .

marcosvital commented 4 years ago

Good! I'll start the final steps towards acceptance.

marcosvital commented 4 years ago

@whedon set 10.21105.joss.01941 as archive

whedon commented 4 years ago

10.21105.joss.01941 doesn't look like an archive DOI.

openjournals / joss-reviews