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[REVIEW]: zalpha: an R package for the identification of regions of the genome under selection #2638

Closed whedon closed 3 years ago

whedon commented 4 years ago

Submitting author: @chorscroft (Clare Horscroft) Repository: https://github.com/chorscroft/zalpha Version: v0.2.0 Editor: @lpantano Reviewers: @juanvillada , @marcrr Archive: 10.5281/zenodo.4301636

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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:

  1. Make sure you're logged in to your GitHub account
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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

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @marcrr

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

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:.

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whedon commented 4 years ago

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<top (required)>' 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

'

juanvillada commented 4 years ago

Hi @lpantano Hi @chorscroft

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

Some notes for now:

  1. The Repository URL is linking to the paper URL (https://github.com/chorscroft/zalpha/tree/master/paper) and not the repository itself.

  2. It looks like the LICENSE is not one of the OSI approved software licenses.

chorscroft commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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<top (required)>' 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

'

chorscroft commented 4 years ago

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!

danielskatz commented 4 years ago

I've changed the URL

danielskatz commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

danielskatz commented 4 years ago

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

juanvillada commented 4 years ago

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.

lpantano commented 4 years ago

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 commented 4 years ago

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

lpantano commented 3 years ago

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

mdogucu commented 3 years ago

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.

lpantano commented 3 years ago

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

stulacy commented 3 years ago

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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aursiber commented 3 years ago

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

juanvillada commented 3 years ago

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:

  1. 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?

  2. 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. 👍🏼 👍🏼 👍🏼

lpantano commented 3 years ago

@whedon add @marcrr as reviewer

whedon commented 3 years ago

OK, @marcrr is now a reviewer

lpantano commented 3 years ago

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

lpantano commented 3 years ago

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

chorscroft commented 3 years ago

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:

  1. 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?

  1. 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:

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.

marcrr commented 3 years ago

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.

chorscroft commented 3 years ago

@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 testcheck("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!

marcrr commented 3 years ago

@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

lpantano 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:

lpantano commented 3 years ago

@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

marcrr commented 3 years ago

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.

lpantano commented 3 years ago

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.

chorscroft commented 3 years ago

@lpantano @marcrr thanks very much to both of you! I have expanded the final paragraph to talk more about the other options available to researchers for running selection scans in R. You were both right, this does read better and make the paper stronger. Thank you very much for your time! Please let me know if there is anything else you'd like me to do.

lpantano 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:

lpantano commented 3 years ago

@marcrr, I see some items uncheck, can you let us know if they are ok now, or any thing else needs to be addressed:

Installation instructions, Automated tests, State of the Field, References

Probably the two last are ok according JOSS guidelines. The two first are required.

Thanks!

marcrr commented 3 years ago

@lpantano I have now checked all the boxes.

Best regards Marc

lpantano commented 3 years ago

@chorscroft, is the package still version: v0.2.0?

chorscroft commented 3 years ago

@lpantano Yes, the version on CRAN is v0.2.0

lpantano commented 3 years ago

@whedon check references

lpantano commented 3 years ago

At this point could you:

I can then move forward with accepting the submission.

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

OK DOIs

- 10.1534/genetics.115.185900 is OK
- 10.1038/ng1001-217 is OK
- 10.1534/genetics.103.025387 is OK
- 10.1007/s00439-017-1847-y is OK
- 10.1101/gr.4252305 is OK
- 10.1093/molbev/msu136 is OK
- 10.1146/annurev-genet-111212-133526 is OK

MISSING DOIs

- 10.1111/1755-0998.12634 may be a valid DOI for title: rehh2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure

INVALID DOIs

- None
lpantano commented 3 years ago

@chorscroft, can you fix that missing DOI, and then go through the list I sent before?thanks!

chorscroft commented 3 years ago

@lpantano I have now updated the doi in the paper, sorry about that! I have also archived the software v0.2.0 on Zenodo and the doi for this is: 10.5281/zenodo.4301636

Please let me know if you need me to do anything else, thanks for your time so far!

lpantano 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

- 10.1111/1755-0998.12634 is OK
- 10.1534/genetics.115.185900 is OK
- 10.1038/ng1001-217 is OK
- 10.1534/genetics.103.025387 is OK
- 10.1007/s00439-017-1847-y is OK
- 10.1101/gr.4252305 is OK
- 10.1093/molbev/msu136 is OK
- 10.1146/annurev-genet-111212-133526 is OK

MISSING DOIs

- None

INVALID DOIs

- None
lpantano commented 3 years ago

@whedon set 10.5281/zenodo.4301636 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4301636 is the archive.

lpantano commented 3 years ago

@whedon accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...