[PRE REVIEW]: MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms #6214

editorialbot · 2024-01-11T23:00:19Z

Submitting author: @sportiellomike (Mike Sportiello)
Repository: https://github.com/sportiellomike/mousebreedeR
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @csoneson
Reviewers: @yjunechoe, @jsun
Managing EiC: Kevin M. Moerman

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editorialbot · 2024-01-11T23:00:22Z

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editorialbot · 2024-01-11T23:00:22Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1210/endocr/bqaa114 is OK
- 10.1371/journal.pone.0012418 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-01-11T23:00:22Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (1432.1 files/s, 134731.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               19            258            255           1132
Markdown                         3            115              0            357
Rmd                              1             27             64             93
TeX                              1              1              0             27
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            25            402            323           1627
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-01-11T23:00:24Z

Wordcount for paper.md is 745

editorialbot · 2024-01-11T23:01:29Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-01-11T23:02:08Z

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Kevin-Mattheus-Moerman · 2024-01-17T12:34:06Z

@sportiellomike I am the AEiC on this track and here to help with initial steps.

I have noticed you use a CC-BY-4.0 license licence. Unfortunately this license is not acceptable for JOSS. You are required to use an OSI approved open source licence.

Kevin-Mattheus-Moerman · 2024-01-17T12:34:38Z

@openjournals/dev it looks like our system did not detect the non-approved licence here. ☝️

sportiellomike · 2024-01-17T16:36:05Z

@Kevin-Mattheus-Moerman my mistake. It has since been updated to the MIT license which is per https://opensource.org/license/mit/. Thank you.

sportiellomike · 2024-01-26T10:05:44Z

@Kevin-Mattheus-Moerman just wanted to check in and see if there's anything you need from me. Thank you.

Kevin-Mattheus-Moerman · 2024-01-26T14:04:37Z

@sportiellomike we are having some difficulties assigning an editor. Quite a few are pre-occupied with other submissions. We are however currently onboard several new editors, so I am hoping one of them will be able to jump in shortly. I'll assign the waitlisted label for now, as we are waiting for an editor to pick this up. Apologies for the delay.

sportiellomike · 2024-01-27T23:46:16Z

@Kevin-Mattheus-Moerman I understand. Just to make sure, did I appropriately change the license? Thank you.

Kevin-Mattheus-Moerman · 2024-01-28T07:59:07Z

@sportiellomike yes the license is now fine thanks.

Kevin-Mattheus-Moerman · 2024-01-28T08:08:09Z

@csoneson I think you might be the best fit for this package. Do you think you could edit it once you are available?

Kevin-Mattheus-Moerman · 2024-01-28T08:08:20Z

@editorialbot invite @csoneson as editor

editorialbot · 2024-01-28T08:08:22Z

Invitation to edit this submission sent!

csoneson · 2024-01-29T12:51:36Z

Sure, I can take this on.
@sportiellomike - thanks for your submission. Before/while I start looking for reviewers, I have a few comments from a first look at your submission:

I would suggest adding some more explanatory text to the vignette - at the moment it's all code chunks with some comments, I think it would be easier to read if there was more actual text helping the reader to understand the code and interpret the output.
It is generally recommended not to depend directly on the tidyverse package (see https://www.tidyverse.org/blog/2018/06/tidyverse-not-for-packages/). Could you depend on individual components instead (also, do you really need it in Depends or could you move it to Imports)?
The repository contains some files that look like they shouldn't be there (deletethese, oldvigs, some R scripts in the main folder), could you clean that up?
I would strongly recommend adding unit tests that check that the package code generates the expected output. Note that this is also one of the points in the JOSS review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html).
Please remove the installation instructions from the paper, the user will get this from the GitHub repository.

csoneson · 2024-01-29T12:51:44Z

@editorialbot assign @csoneson as editor

editorialbot · 2024-01-29T12:51:47Z

Assigned! @csoneson is now the editor

sportiellomike · 2024-01-30T04:17:10Z

Thank you @csoneson for your helpful comments!

Vignette edited!
Changed dependency for tidyverse!
Cleaned up folder!
Added tests!
Removed installation section from paper and am about to regenerate file for JOSS!

Thanks again!

sportiellomike · 2024-01-30T04:17:42Z

@editorialbot generate pdf

editorialbot · 2024-01-30T04:18:41Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2024-01-30T04:19:19Z

Five most similar historical JOSS papers:

GeneNetwork: framework for web-based genetics
Submitting author: @pjotrp
Handling editor: @arfon (Active)
Reviewers: @krother, @agarie
Similarity score: 0.8433

Bedtoolsr: An R package for genomic data analysis and manipulation
Submitting author: @dphansti
Handling editor: @mgymrek (Retired)
Reviewers: @nhejazi, @mikmaksi
Similarity score: 0.8307

rTASSEL: An R interface to TASSEL for analyzing genomic diversity
Submitting author: @btmonier
Handling editor: @fboehm (Active)
Reviewers: @tkchafin, @tomsing1
Similarity score: 0.8300

REGENS: an open source Python package for simulating realistic autosomal genotypes
Submitting author: @greggj2016
Handling editor: @fboehm (Active)
Reviewers: @raivivek, @dwinter
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geneXplainR: An R interface for the geneXplain platform
Submitting author: @pstegma
Handling editor: @mgymrek (Retired)
Reviewers: @selbouhaddani
Similarity score: 0.8285

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

csoneson · 2024-01-30T22:21:03Z

@sportiellomike Great, thanks - I'll start looking for suitable reviewers. If you have suggestions (see the first post above), feel free to mention them here.

csoneson · 2024-02-04T15:20:09Z

👋🏻 @JoanyMarino, @btmonier, @mkerin - would you be interested in reviewing this submission for JOSS?

#6214

Thanks in advance!

csoneson · 2024-02-12T15:30:06Z

👋🏻 @yjunechoe, @Balexandre23 (or @JoanyMarino, @btmonier, @mkerin) - would you be interested in reviewing this submission for the Journal of Open Source Software (JOSS)?

#6214

Thanks a lot in advance!

yjunechoe · 2024-02-12T16:46:57Z

I am happy to review, though please note that I do not have domain expertise in this area (of biology). I will limit my comments to the quality of the R code.

I'd also like to note a couple immediate concerns from a cursory look at the codebase:

The package (still) imports the entire tidyverse suite of packages. Functions from external dependencies (e.g., bind_rows() from dplyr) are not appropriately imported or namespaced where they are used within the package.
NAMESPACE exports everything, and does not discriminate between user facing and internal functions
Code in @examples are not minimally reproducible examples
Code in /tests contain unnecessary copy-pasted code and do not isolate unit tests
Documentation files in /man contain what I presume to be leftovers from previous versions of the package (e.g., hello.Rd)

Speaking for myself as a potential reviewer, I don't think this package is quite ready for review. I would like for at least these issues to be resolved before I personally dedicate more time to reviewing the actual functionalities of the package. In sum, I conditionally accept to be a reviewer.

sportiellomike · 2024-02-13T02:48:19Z

Thank you @yjunechoe for your time,

I think I am misunderstanding something here, since I was asked to move it to imports which I did (see above thread). Could you help me understand what you mean?
I used the roxygen2 (https://cran.r-project.org/web/packages/roxygen2/vignettes/roxygen2.html) to help create the package, as described in most R packages, which created a default NAMESPACE. Is there utility in editing it?
The code in @examples follows the vignette's naming conventions to walk the user through the process. Should I make sure the @example has extra lines in it analogous to the vignette to make reproducible?
The tests I created attempted to make sure the package's main arguments worked successfully. Would it be better if I made sure the function tested got a specific value each time that I have preset?
hello.Rd should have been deleted, and that was my mistake for missing that. It is now corrected.

yjunechoe · 2024-02-13T03:41:21Z

Thank you for the quick response addressing my comments - I'll answer your questions in turn:

It is indeed an improvement to move a dependency from Depends to Imports, but this still misses the bigger issue about depending on the entire tidyverse metapackage (Imports still creates a dependency - for more on the technical details, see https://r-pkgs.org/dependencies-in-practice.html#sec-dependencies-in-imports). The package should specifically Import only the packages necessary for it to function - and in fact, since the package already Imports dplyr and ggplot2, that may be sufficient on their own.

I would highly advise using @export tags for each function that you plan to export, but perhaps this not so critical for a package of this (small) scale. I will take this back for the moment and evaluate the necessity of this in the actual review.

I mean that simple, one-liner examples with no setup like this:

#' @examples
#' compilegametes(engageinmeiosisoutput)

cannot be ran by the user after installing and loading the package (what is the engageinmeiosisoutput here and where is it defined?). This makes it very difficult to evaluate the functionalities of the functions in the package as a reviewer, and constitutes incomplete documentation of a function's behavior. Please ensure that all code in @examples includes the necessary setup such that they can be ran as-is, once the package has been loaded.

As I have not yet fully evaluated the scope of the package's features, I will also take this back for the moment. But I would advise you to consult existing materials on writing unit tests in R to increase the number and kind of unit tests (e.g., https://r-pkgs.org/testing-design.html), to receive a better evaluation of the test suite in the review (tests should not only cover correctness, but also edge cases, the signaling of appropriate messages and warnings, etc.). In any case, I can say more on what I expect to see from tests in the actual review.

Please address (1) and (3) and I am happy to formally review the package.

sportiellomike · 2024-02-13T04:03:33Z

@yjunechoe ,

Thanks for your explanations. I will address these points as soon as I am able and update you by tagging you here after. Thank you.

csoneson · 2024-02-14T21:14:29Z

Thanks @yjunechoe for (conditionally) accepting and for your initial comments.

csoneson · 2024-02-21T13:31:09Z

Just for the record - in parallel I'm reaching out to potential reviewers offline/over email.

csoneson · 2024-03-04T19:23:15Z

👋🏻 @RobLBaker - would you be interested in reviewing this submission for JOSS?

#6214

Thanks in advance!

sportiellomike · 2024-03-05T02:24:32Z

@yjunechoe, thank you for your first round of suggestions. I believe I have responded to the ones you requested (1 and 3). Thanks to your advice, I have removed the dependency of tidyverse, created example data that should help users when they look up functions, cleaned up a couple of miscellaneous things, and retested.

csoneson · 2024-03-08T16:09:29Z

👋🏻 @greggj2016, @dwinter, @tkchafin - would you be willing to review this submission for the Journal of Open Source Software (JOSS)?

#6214

Many thanks in advance!

tkchafin · 2024-03-08T16:25:34Z

Sorry, I can't take on another review just now. I suggest igorkf as a possible alternative

RobLBaker · 2024-03-08T16:45:22Z

Unfortunately I also don't have the time at the moment. In addition, github is being blocked by my work computer.

…

-Rob Robert Baker, Ph.D. (he/him) Data Scientist/Integrative Biologist National Park Service Inventory & Monitoring Division 1201 Oakridge Drive, Suite 150 Fort Collins, CO 80525 970-267-7216 (office) From: Tyler Chafin ***@***.***> Sent: Friday, March 8, 2024 9:26 AM To: openjournals/joss-reviews ***@***.***> Cc: Baker, Robert L ***@***.***>; Mention ***@***.***> Subject: [EXTERNAL] Re: [openjournals/joss-reviews] [PRE REVIEW]: MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms (Issue #6214) This email has been received from outside of DOI - Use caution before clicking on links, opening attachments, or responding. Sorry, I can't take on another review just now. I suggest igorkf as a possible alternative - Reply to this email directly, view it on GitHub<#6214 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AXIIC7L5A2BEO2IJV5JQCV3YXHRBLAVCNFSM6AAAAABBXIBTZOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBVHE4TSNZVG4>. You are receiving this because you were mentioned.Message ID: ***@***.***>

csoneson · 2024-03-08T18:11:17Z

👋🏻 @igorkf - would you be willing to review this submission for the Journal of Open Source Software (JOSS)?

#6214

Our review takes places openly on GitHub and is checklist-based, see here for more details.

Many thanks in advance!

greggj2016 · 2024-03-08T18:18:35Z

Sorry, I can't do that right now.

…

On Fri, Mar 8, 2024 at 11:09 AM Charlotte Soneson ***@***.***> wrote: 👋🏻 @greggj2016 <https://github.com/greggj2016>, @dwinter <https://github.com/dwinter>, @tkchafin <https://github.com/tkchafin> - would you be willing to review this submission for the Journal of Open Source Software (JOSS)? MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms #6214 <#6214> Many thanks in advance! — Reply to this email directly, view it on GitHub <#6214 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKJ677M7QXANOJSLFHNKV33YXHPFDAVCNFSM6AAAAABBXIBTZOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBVHE3DQNZTGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

igorkf · 2024-03-11T00:31:47Z

Sorry, I can't do it right now.

csoneson · 2024-03-11T18:05:55Z

👋🏻 @sdhutchins, @jsun, @tgerke - would you be willing to review this submission for the Journal of Open Source Software (JOSS)?

#6214

Our review takes places openly on GitHub and is checklist-based, see here for more details.

Many thanks in advance!

jsun · 2024-03-12T23:45:23Z

fine!

csoneson · 2024-03-13T05:42:32Z

Thank you @jsun!

@yjunechoe - could you confirm that you are still willing to review this submission? Then I will assign you both and open the review issue.

yjunechoe · 2024-03-13T11:25:35Z

Yes!

csoneson · 2024-03-13T11:49:56Z

Brilliant, thanks!

csoneson · 2024-03-13T11:50:37Z

@editorialbot add @yjunechoe as reviewer

editorialbot · 2024-03-13T11:50:40Z

@yjunechoe added to the reviewers list!

csoneson · 2024-03-13T11:50:44Z

@editorialbot add @jsun as reviewer

editorialbot · 2024-03-13T11:50:46Z

@jsun added to the reviewers list!

csoneson · 2024-03-13T11:51:00Z

@editorialbot start review

editorialbot · 2024-03-13T11:51:03Z

OK, I've started the review over in #6474.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jan 11, 2024

editorialbot added R TeX labels Jan 11, 2024

Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jan 26, 2024

editorialbot assigned csoneson Jan 29, 2024

editorialbot assigned yjunechoe Mar 13, 2024

editorialbot assigned jsun Mar 13, 2024

editorialbot closed this as completed Mar 13, 2024

[PRE REVIEW]: MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms #6214

[PRE REVIEW]: MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms #6214

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