search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
712 stars 38 forks source link

[REVIEW]: latentcor: An R Package for estimating latent correlations from mixed data types #3634

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @muellsen (Christian Lorenz Müller) Repository: https://github.com/mingzehuang/latentcor Version: v1.1.0 Editor: @crvernon Reviewer: @corybrunson, @rmflight Archive: 10.5281/zenodo.5517823

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4a6c419d1fb73148cbf13881b97c5ba9"><img src="https://joss.theoj.org/papers/4a6c419d1fb73148cbf13881b97c5ba9/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4a6c419d1fb73148cbf13881b97c5ba9/status.svg)](https://joss.theoj.org/papers/4a6c419d1fb73148cbf13881b97c5ba9)

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

@corybrunson & @rmflight , 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @crvernon know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @corybrunson

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @rmflight

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @corybrunson, @rmflight it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

: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:

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

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

@whedon generate pdf
whedon commented 3 years ago

Wordcount for paper.md is 1567

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.10 s (449.5 files/s, 64825.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             8            332             92           1825
R                               17            114            387            930
XML                              1              0              2            441
CSS                              3             99             48            428
JavaScript                       4             64             34            266
Markdown                         2             59              0            193
TeX                              2              6              0            168
YAML                             3             23              2            115
Rmd                              1            146            452             64
SVG                              1              0              1             11
Bourne Shell                     2              6             30              8
-------------------------------------------------------------------------------
SUM:                            44            849           1048           4449
-------------------------------------------------------------------------------

Statistical information for the repository '683689bce2b9e81299405bea' was
gathered on 2021/08/19.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Mingze Huang                     3         35945          35581          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Mingze Huang                364            1.0          0.0                9.34
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/biomet/asaa007 is OK
- 10.1080/00401706.2012.727746 is OK
- 10.1111/rssb.12168 is OK
- 10.1080/10618600.2021.1882468 is OK
- 10.21105/joss.02306 is OK
- 10.3389/fgene.2019.00516 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

crvernon commented 3 years ago

@corybrunson @rmflight @muellsen :wave: the review takes place in this issue. Thanks!

crvernon commented 3 years ago

Also, please don't forget to add a link to this review issue in any issues or pull requests you may generate in the https://github.com/mingzehuang/latentcor repository. This will help everyone have a single point of reference.

crvernon commented 3 years ago

:mega: Mid-week rally! Just checking in to see how things are going.

:open_hands: @corybrunson @rmflight I am happy to answer any questions you may have!

Have a great rest of the week!

rmflight commented 3 years ago

Getting it installed in an renv so I can start evaluating. Just finally got settled in for vacation, so I should be able to start taking a look today.

crvernon commented 3 years ago

Sounds great @rmflight ! Thanks!

corybrunson commented 3 years ago

I've successfully installed the package and run some basics. I plan to conduct the full review next week. : )

crvernon commented 3 years ago

@corybrunson sounds great! Thanks for the update!

rmflight commented 3 years ago

Issues around documentation / API:

rmflight commented 3 years ago

Issues around missing files for an OSS project:

rmflight commented 3 years ago

@crvernon, where is the draft of the manuscript in final form? I tried the links in this issue, and they both give me a 404, and searching the JOSS paper archive gives no results. Can I just ask whedon for it here?

crvernon commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

crvernon commented 3 years ago

☝️ Here you go @rmflight

rmflight commented 3 years ago

Issues around the paper itself:

rmflight commented 3 years ago

The current manuscript shows some of the things I'd like to see in another vignette, and shows that the software runs properly, and I've verified it can run, and it has tests, so I think I'm done for a first round.

My verdict is Major Revisions. Please feel free to ask for more clarification on the issues if they aren't clear.

crvernon commented 3 years ago

:mega: Hello all! It looks like @rmflight and @corybrunson have made good progress on the review! Also, great work @mingzehuang and @irinagain in addressing their issues as they arise.

Just a reminder for the reviewers: don't forget to check off the reviewer checklist as you feel your comments have been sufficiently addressed. Also, once you believe your review to be completed, shoot me a comment here.

👏 Great progress everyone and keep up the good work! Let's keep driving towards getting this software publication ready!

whedon commented 3 years ago

:wave: @rmflight , please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @corybrunson, please update us on how your review is going (this is an automated reminder).

corybrunson commented 3 years ago

Good timing! I'm resuming my review now. : )

corybrunson commented 3 years ago

The package is quite easy to use and i fully intend to make use of it myself, so i thank the authors for creating it! I have reviewed the package and the paper and raised all issues that occurred to me. I may raise more as others are addressed, but for the time being i welcome responses (whether revisions or feedback) from the authors. : )

crvernon commented 3 years ago

Excellent! Thanks @corybrunson !

crvernon commented 3 years ago

:mega: Mid-week rally! Looks like we have some active issues that progress is being made on @irinagain , @muellsen , and @mingzehuang !

Thanks @corybrunson and @rmflight for providing your feedback so far!

👏 Keep up the good work!

irinagain commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

irinagain commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

corybrunson commented 3 years ago

@crvernon the issues i raised have been addressed and i have completed my review, though i welcome the opportunity to review further revisions while the review remains open.

crvernon commented 3 years ago

Fantastic @corybrunson ! Thanks for your volunteering your time and providing a thoughtful review!

mingzehuang commented 3 years ago

Thank you so much @corybrunson and @crvernon !

mingzehuang commented 3 years ago

Thank you so much for all of your comments @rmflight ! We've replied on all issues:) Let us know anything need to be improved:)

rmflight commented 3 years ago

Apologies for taking so long to finish looking at the responses to my issues.

I believe everything I brought up has been addressed. The authors have an awesome package, and I definitely have some more background reading to do on the different correlation measures.

mingzehuang commented 3 years ago

Thank you so much Dr. @rmflight ! We appreciate your great help!

crvernon commented 3 years ago

Thanks for your volunteering your time and providing a thoughtful review @rmflight !

crvernon commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

crvernon commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/biomet/asaa007 is OK
- 10.1080/00401706.2012.727746 is OK
- 10.1111/rssb.12168 is OK
- 10.1080/10618600.2021.1882468 is OK
- 10.21105/joss.02306 is OK
- 10.3389/fgene.2019.00516 is OK

MISSING DOIs

- 10.1214/12-aos1041 may be a valid DOI for title: Regularized rank-based estimation of high-dimensional nonparanormal graphical models

INVALID DOIs

- None
crvernon commented 3 years ago

@mingzehuang please add the following missing DOI to your citation in the paper:

- 10.1214/12-aos1041 may be a valid DOI for title: Regularized rank-based estimation of high-dimensional nonparanormal graphical models
crvernon commented 3 years ago

@mingzehuang - Your paper is looking great - and very clean I might add! Here are several things I would like you to address from my review of your paper before we move on:

mingzehuang commented 3 years ago

@whedon check references

whedon commented 3 years ago

Downloading of the repository (to check the bibtex) failed for issue #3634 failed with the following error: 

Cloning into '0a3575676979d9b378be5a4d'...
mingzehuang commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mingzehuang commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/biomet/asaa007 is OK
- 10.1080/00401706.2012.727746 is OK
- 10.1111/rssb.12168 is OK
- 10.1080/10618600.2021.1882468 is OK
- 10.21105/joss.02306 is OK
- 10.3389/fgene.2019.00516 is OK
- 10.1214/12-aos1041 is OK

MISSING DOIs

- None

INVALID DOIs

- None