[PRE REVIEW]: GGoutlieR: an R package to identify and visualize unusual geo-genetic patterns of biological samples

[editorialbot]

Submitting author: !--author-handle-->@CheWeiChang1992<!--end-author-handle-- (Che-Wei Chang) Repository: https://github.com/kjschmidlab/GGoutlieR Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@martinfleis<!--end-editor-- Reviewers: @tkchafin, @btmartin721 Managing EiC: Kevin M. Moerman

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Author instructions

Thanks for submitting your paper to JOSS @CheWeiChang1992. Currently, there isn't a JOSS editor assigned to your paper.

@CheWeiChang1992 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (1021.4 files/s, 183025.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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R                               13            207            462           1867
TeX                              3             84             15            514
Markdown                         2             40              0            144
Rmd                              1             82            179            120
make                             1              6              0             20
YAML                             1              1              4             18
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SUM:                            21            420            660           2683
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gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1038/s41559-021-01526-9 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1371/journal.pgen.1005703 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.7554/eLife.54507 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1093/bioinformatics/btv703 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41477-020-0659-6 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/1755-0998.12747 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.3389/fpls.2020.00701 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1093/plcell/koac267 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/mec.15169 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cell.2020.05.023 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41588-018-0266-x is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41588-022-01189-7 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41586-018-0063-9 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/ng.2285 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

Wordcount for paper.md is 1195

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@CheWeiChang1992 thanks for this submission. I am the AEiC on this track and here to help process initial steps. For the moment can you try to address the following:

• [x] Please fix the potentially missing/invalid DOIs pointed out above :point_up: , you can call @editorialbot check references to check them again, and use @editorialbot generate pdf to update the paper.
• [x] Our system did not detect an open source license. Please can you clarify what license your software uses? Also I recommend you add a plain text LICENSE file in the main directory of your repository.

[CheWeiChang1992]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.7554/eLife.54507 is OK
- 10.1093/bioinformatics/btv703 is OK
- 10.1038/s41477-020-0659-6 is OK
- 10.1111/1755-0998.12747 is OK
- 10.3389/fpls.2020.00701 is OK
- 10.1093/plcell/koac267 is OK
- 10.1111/mec.15169 is OK
- 10.1016/j.cell.2020.05.023 is OK
- 10.1038/s41588-018-0266-x is OK
- 10.1038/s41588-022-01189-7 is OK
- 10.1038/s41586-018-0063-9 is OK
- 10.1038/ng.2285 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1038/s41559-021-01526-9 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1371/journal.pgen.1005703 is INVALID because of 'https://doi.org/' prefix

[CheWeiChang1992]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41559-021-01526-9 is OK
- 10.1371/journal.pgen.1005703 is OK
- 10.7554/eLife.54507 is OK
- 10.1093/bioinformatics/btv703 is OK
- 10.1038/s41477-020-0659-6 is OK
- 10.1111/1755-0998.12747 is OK
- 10.3389/fpls.2020.00701 is OK
- 10.1093/plcell/koac267 is OK
- 10.1111/mec.15169 is OK
- 10.1016/j.cell.2020.05.023 is OK
- 10.1038/s41588-018-0266-x is OK
- 10.1038/s41588-022-01189-7 is OK
- 10.1038/s41586-018-0063-9 is OK
- 10.1038/ng.2285 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[CheWeiChang1992]

@editorialbot generate pdf

[editorialbot]

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

[CheWeiChang1992]

@Kevin-Mattheus-Moerman Thank you very much for your assistance.

1. I've solved the invalid DOIs detected by the editorial bot. I also checked references with @editorialbot check references and update PDF with @editorialbot generate pdf as you suggested.
2. Our MIT LICENSE is located at ./ggoutlier/LICENSE, probably that is why the editorial bot could not find it. I've made a copy of LICENSE in the main directory. Let me know if there is anything that should be fixed. Thank you.

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

Thanks @CheWeiChang1992 for making those changes. Note I have just flagged this submission for scope review by the editorial board. This is mainly to check if the software conforms to our substantial scholarly effort criteria in terms of both size and functionality. This review should be completed within 2 weeks.

[Kevin-Mattheus-Moerman]

@CheWeiChang1992

The scope review has concluded this work may be in scope for JOSS. However, as part of the scope review, the following was pointed out:

The GitHub repository is not set up in such a way that one can install it as one would normally do, because the package itself is hidden in the sub-directory named ggoutlier. In addition, it is not on CRAN, which is definitely a minus.

Can you please address these points before we proceed? Thanks.

[Kevin-Mattheus-Moerman]

@editorialbot assign @martinfleis as editor

[editorialbot]

Assigned! @martinfleis is now the editor

[CheWeiChang1992]

@CheWeiChang1992

The scope review has concluded this work may be in scope for JOSS. However, as part of the scope review, the following was pointed out:

The GitHub repository is not set up in such a way that one can install it as one would normally do, because the package itself is hidden in the sub-directory named ggoutlier. In addition, it is not on CRAN, which is definitely a minus.

Can you please address these points before we proceed? Thanks.

Thank you very much for pointing out the issues.

• I moved the package to the main directory, so now it is able to be installed with the install_github function in the R package devtools.
• I submitted the package to CRAN and it is now waiting for manual review by the CRAN team (see below). I'll update you if there is any news.

  Dear maintainer, package GGoutlieR_1.0.0.tar.gz has been auto-processed and is pending a manual inspection of this new CRAN submission. A CRAN team member will typically respond to you within the next 10 working days. For technical reasons you may receive a second copy of this message when a team member triggers a new check. Log dir: https://win-builder.r-project.org/incoming_pretest/GGoutlieR_1.0.0_20230601_151744/ The files will be removed after roughly 7 days. Installation time in seconds: 7 Check time in seconds: 93 R Under development (unstable) (2023-05-31 r84480 ucrt)

[martinfleis]

@CheWeiChang1992 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list). Genetics is a bit out of my comfort zone, so I'd appreciate some helping hand here :). Thanks!

[CheWeiChang1992]

@CheWeiChang1992 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list). Genetics is a bit out of my comfort zone, so I'd appreciate some helping hand here :). Thanks!

Thank you for the information. We would like to suggest the following scientists in the field of landscape genomics as potential reviewers:

• Geoffrey House and/or Matthew Hahn (github user name: hahnlab-user)
• Gideon Bradburd (github user name: gbradburd)
• Peter Ralph (github user name: petrelharp)

For the list of JOSS reviewers (https://bit.ly/joss-reviewers), it seems that I need access. I sent a request for the list through my private Google account (jerry122116@gmail.com). I'd be grateful if you could confirm my access request. I can then have a look at the list. Thank you for your assistance!

[martinfleis]

Sorry! The list of JOSS reviewers is now here https://reviewers.joss.theoj.org/reviewers. Can you check that one?

[CheWeiChang1992]

Sorry! The list of JOSS reviewers is now here https://reviewers.joss.theoj.org/reviewers. Can you check that one?

Thank you for the JOSS reviewer list.

I selected three people from the list who may be suitable as potential reviewers.

• Tyler Chafin (github name: tkchafin)
• Maximilian Hesselbarth (github name: mhesselbarth)
• David Winter (github name: dwinter)

By the way, now the package is available on the CRAN. Please let me know if you have any suggestions. Thank you!

[martinfleis]

Hi @tkchafin, @mhesselbarth, @dwinter,

would you be willing to help here and review this submission to JOSS? After reviewing the suggestions, I believe it would be a good fit for you.

Thank you!

[tkchafin]

Hi @martinfleis yes this looks like something I could review.

[martinfleis]

@editorialbot add @tkchafin as reviewer

@tkchafin thank you! And especially for a swift response.

[editorialbot]

@tkchafin added to the reviewers list!

[Winter]

Sorry! The list of JOSS reviewers is now here https://reviewers.joss.theoj.org/reviewers. Can you check that one?

Thank you for the JOSS reviewer list.

I selected three people from the list who may be suitable as potential reviewers.

• Tyler Chafin (github name: tkchafin)
• Maximilian Hesselbarth (github name: mhesselbarth)
• David Winter (github name: winter)

By the way, now the package is available on the CRAN. Please let me know if you have any suggestions. Thank you!

Hey Che-Wei Chang!

You may want to get in contact with David Winter to confirm his GitHub handle as I'm not David :)

Best Regards, Edward (@Winter)

[CheWeiChang1992]

Sorry! The list of JOSS reviewers is now here https://reviewers.joss.theoj.org/reviewers. Can you check that one?

Thank you for the JOSS reviewer list. I selected three people from the list who may be suitable as potential reviewers.

• Tyler Chafin (github name: tkchafin)
• Maximilian Hesselbarth (github name: mhesselbarth)
• David Winter (github name: winter)

By the way, now the package is available on the CRAN. Please let me know if you have any suggestions. Thank you!

Hey Che-Wei Chang!

You may want to get in contact with David Winter to confirm his GitHub handle as I'm not David :)

Best Regards, Edward (@Winter)

@Winter Sorry for my mistake. I'll fix it.

[mhesselbarth]

Sorry, but I am completely missing the genetics background to be able to review this.

[martinfleis]

Hi @tgerke, would you be able to review this submission to JOSS?

[tkchafin]

If you aren't able to find a second reviewer, I have a colleague (Bradley Martin: @btmartin721) that has the right background for this and might be interested in reviewing it.

[martinfleis]

@tkchafin thanks!

@btmartin721 would you be willing to review this package for JOSS?

[btmartin721]

My apologies for my late reply. I would be willing to review it.

[martinfleis]

@editorialbot add @btmartin721 as reviewer

Thanks a lot @btmartin721!

[editorialbot]

@btmartin721 added to the reviewers list!

[martinfleis]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5687.