Joss-reviews: [REVIEW]: zalpha: an R package for the identification of regions of the genome under selection

Created on 4 Sep 2020 · 32Comments · Source: openjournals/joss-reviews

Submitting author: @chorscroft (Clare Horscroft)
Repository: https://github.com/chorscroft/zalpha
Version: v0.2.0
Editor: @lpantano
Reviewers: @juanvillada , @marcrr
Archive: Pending

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Status

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Markdown: [![status](https://joss.theoj.org/papers/192e6116cb058784d448090a81fdf3aa/status.svg)](https://joss.theoj.org/papers/192e6116cb058784d448090a81fdf3aa)

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

@juanvillada , 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 @lpantano 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 @juanvillada

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 (@chorscroft) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 @marcrr

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 (@chorscroft) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] 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

[x] 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.
[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)?
[ ] 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?
[ ] 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)?
[ ] 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?

R TeX review

Source

whedon

Most helpful comment

thanks @marcrr, I got update from the BoE, and it seems enough to mention the tools so the reader has an idea where to go to learn more about the field. Since there is a description of the method already, we agreed this is almost enough.
@chorscroft, do you think you could add a little more about the other packages, if they target a different context, or they have some limitations your package doesn't, or a limitation of your package that the others can do? I think a couple of more sentences about the limitations and context for each should be enough to accept this. Thanks.

lpantano on 18 Nov 2020

👍2

All 32 comments

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

:warning: JOSS reduced service mode :warning:

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whedon on 4 Sep 2020

PDF failed to compile for issue #2638 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2638 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon/processor.rb:61:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/bin/whedon:119:in from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

whedon on 4 Sep 2020

Hi @lpantano
Hi @chorscroft

The PDF failed to compile. I will resume my review once it has been fixed.

Some notes for now:

The Repository URL is linking to the paper URL (https://github.com/chorscroft/zalpha/tree/master/paper) and not the repository itself.
It looks like the LICENSE is not one of the OSI approved software licenses.

juanvillada on 9 Sep 2020

@whedon generate pdf

chorscroft on 9 Sep 2020

PDF failed to compile for issue #2638 with the following error:

whedon on 9 Sep 2020

How odd, it compiled on the original thread for danielskatz on Aug 9th and I haven't changed anything! https://github.com/openjournals/joss-reviews/issues/2560

The licence is an MIT licence, I thought that was okay? Please let me know if it's not!
https://github.com/chorscroft/zalpha/blob/master/LICENSE.md
https://opensource.org/licenses/MIT

And apologies for linking to the wrong place, the submission form says "URL of the submitted software's git repository (containing the paper)" so I thought it was supposed to be a link to the paper in the software repository not the software itself, my fault. How can I fix it?

Thanks!

chorscroft on 9 Sep 2020

👍1

I've changed the URL

danielskatz on 9 Sep 2020

👍2

@whedon generate pdf

danielskatz on 9 Sep 2020

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

whedon on 9 Sep 2020

I think I changed the URL manually in the pre-review issue, but it was set back in this review issue

danielskatz on 9 Sep 2020

👍2

How odd, it compiled on the original thread for danielskatz on Aug 9th and I haven't changed anything! #2560

Excellent! The PDF of the paper looks good now. Thanks @danielskatz ✅

The licence is an MIT licence, I thought that was okay? Please let me know if it's not!
https://github.com/chorscroft/zalpha/blob/master/LICENSE.md
https://opensource.org/licenses/MIT

Yes, that one is ok. ✅
I just got confused with the other license file in the repo (https://github.com/chorscroft/zalpha/blob/master/LICENSE).

I will resume my review.

juanvillada on 9 Sep 2020

Hi @juanvillada and @chorscroft, I am having difficulties finding a second reviewer, if you have a name in your mind, let me know. Thanks!

lpantano on 14 Sep 2020

Hi @aursiber, would you like to review this paper? https://joss.readthedocs.io/en/latest/review_checklist.html

lpantano on 14 Sep 2020

Hi @stulacy, @mdogucu, @nhejazi, would any of you like to review this tool?

lpantano on 22 Sep 2020

Thank you for considering me but I have never worked with genome data in my life. I think there is something unusual with review requests I get from JOSS and I am wondering how I can correct it. Either I have made a mistake in filing my areas of interest or JOSS is sending me random review requests. Is there any place I can update my reviewer settings for JOSS and edit my areas of expertise etc. ? I understand that finding reviewers is extremely difficult so I hope to ease the process for both the editors and myself.

Thank you @lpantano and everyone else who puts the time to run JOSS.

mdogucu on 22 Sep 2020

Thank you @mdogucu , sorry about this. I will make the request!

lpantano on 22 Sep 2020

Sorry, this is quite far out of my field

On Tue, 22 Sep 2020 at 21:41, Lorena Pantano notifications@github.com
wrote:

Thank you @mdogucu https://github.com/mdogucu , sorry about this. I
will make the request!

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stulacy on 23 Sep 2020

Sorry for the delay in responding. I have no competence in genomics to review this work.

Hi @aursiber, would you like to review this paper? https://joss.readthedocs.io/en/latest/review_checklist.html

aursiber on 23 Sep 2020

The paper is well-written and references are appropriate. The authors make a good contribution to the field by building an open source software (R package) relevant to the identification of selective sweep in genomic regions. The package delivers what it aims. Overall, I think the paper is worth of publication.

Minor issues:

There are 4 co-authors listed on the paper while only one appears as the sole contributor of the software. I leave this consideration to the Editor (@lpantano) as I understand this is pretty normal in academic papers. Please see:

Contribution and authorship: Has the submitting author (@chorscroft) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
The community guidelines are not explicit in the package repository. Please see:

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

Thanks @chorscroft and colleagues for making this OSS. 👍🏼 👍🏼 👍🏼

juanvillada on 27 Sep 2020

@whedon add @marcrr as reviewer

lpantano on 5 Oct 2020

OK, @marcrr is now a reviewer

whedon on 5 Oct 2020

Hey @marcrr, do you have an update on this? Thanks!

lpantano on 26 Oct 2020

Hey @chorscroft, can you comment on @juanvillada comments? Thanks!

lpantano on 26 Oct 2020

The paper is well-written and references are appropriate. The authors make a good contribution to the field by building an open source software (R package) relevant to the identification of selective sweep in genomic regions. The package delivers what it aims. Overall, I think the paper is worth of publication.

Minor issues:

There are 4 co-authors listed on the paper while only one appears as the sole contributor of the software. I leave this consideration to the Editor (@lpantano) as I understand this is pretty normal in academic papers. Please see:

Contribution and authorship: Has the submitting author (@chorscroft) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

The community guidelines are not explicit in the package repository. Please see:

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

Thanks @chorscroft and colleagues for making this OSS. 👍🏼 👍🏼 👍🏼

Thank you @juanvillada for putting the time and effort to review my paper!

Apologies for the slow response, I wasn't sure if I was supposed to wait for all the reviews to be returned.

Response to issue 1:
Thanks for raising this point! I created the software and coded it all myself, however my co-authors have been invaluable to the project by:

testing the code
reading the documentation
developing the statistics used in the code
contributing knowledge about the science and biology behind the statistics
reading and editing the text of the paper
It is standard in my field to include these people as authors on the paper.

Response to issue 2:
Thank you very much for bringing this to my attention, you are correct that these things were not explicit. I have now included a "Community Guidelines" section in the README file with instructions on how to raise issues, report bugs and seek support, as well as how to contribute via pull requests.

Thank you to everyone who has been involved in reviewing and editing this paper so far.

chorscroft on 29 Oct 2020

👍1

Sorry for the delay in writing this review.

Overall, this is a nice software and a nice contribution. It was easy to install and run. I have a few points, which I will structure following the Review checklist.

An small point: it would be nice to provide the compiled PDF for easier access by readers.

Installation instructions: Is there a clearly-stated list of dependencies

It was easy to install the dependencies, but I did not find them listed in one place. Following the criteria of the journal, it might be good to list them clearly somewhere.

Automated tests

I was unable to run test_check("zalpha") nor to find any reference to it in the documentation. Maybe I missed something? Could @chorscroft clarify whether there is an automated test, and whether this is it please?

State of the field: Do the authors describe how this software compares to other commonly-used packages?

This is my largest concern, the paper does not present any comparison to other software. There are many R packages which compute LD in some way or another.
The same concern applies to References.

marcrr on 30 Oct 2020

👍1

@marcrr, thank you very much for the time and effort you put into reviewing our paper!

_An small point: it would be nice to provide the compiled PDF for easier access by readers._

Thanks for this point - I have now uploaded a pdf version of the paper to the repository.

Installation instructions: Is there a clearly-stated list of dependencies
_It was easy to install the dependencies, but I did not find them listed in one place. Following the criteria of the journal, it might be good to list them clearly somewhere._

Thank you for raising this point. There actually aren’t any required dependencies for this package; however, I have written a section into the README file to state the minimum R version required and to list the optional packages so users can be aware in advance.

Automated tests
_I was unable to run test_check("zalpha") nor to find any reference to it in the documentation. Maybe I missed something? Could @chorscroft clarify whether there is an automated test, and whether this is it please?_

Thank you for this point. The package does contain a suite of tests but they were inaccessible to the user. I have now created a Travis-CI account and linked the github repository and there is a badge in the README file to show the status. Travis-CI checks all the test whenever there is a push to the github repository. I hope this addresses this point.

State of the field: Do the authors describe how this software compares to other commonly-used packages?
_This is my largest concern, the paper does not present any comparison to other software. There are many R packages which compute LD in some way or another.
The same concern applies to References._

Thank you for raising this issue. I have added a paragraph with references to other packages that use similar methods to perform selection scans.

Thanks again for your review, it was very helpful!

chorscroft on 9 Nov 2020

👍1

@chorscroft Thank you for your revisions. They reply to almost all my concerns.

I still find the comparison to other packages very light, even with the new paragraph. I am not sure what the standards are for this journal, so I will let @lpantano make the final call on this.

Best regards
Marc

marcrr on 12 Nov 2020

👍1

@whedon generate pdf

lpantano on 16 Nov 2020

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

whedon on 16 Nov 2020

@marcrr. @chorscroft, I am checking with the editorial board about the amount of information when comparing with other packages. @marcrr, if you know other packages that are not there, feel free to mention it here. Even if we decides we don't need a lot, it would be good to have the best list possible and maybe we just ask for a little more information for each package. Thanks

lpantano on 16 Nov 2020

From my point of view, it's less a question of specific other packages, than of discussing the relative advantages of the new package in a bit more detail.

marcrr on 17 Nov 2020

lpantano on 18 Nov 2020

👍2

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