editorialbot commented 10 months ago

Submitting author: !--author-handle-->@smasongarrison@osorensen<!--end-editor-- Reviewers: @wjakethompson, @mhu48 Archive: 10.6084/m9.figshare.25238536

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/ee3a025be4f61584f977a7657d936187/status.svg)](https://joss.theoj.org/papers/ee3a025be4f61584f977a7657d936187)

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

@wjakethompson & @mhu48, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen 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 ✨

Checklists

📝 Checklist for @mhu48

📝 Checklist for @wjakethompson

editorialbot commented 10 months ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

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

@editorialbot generate pdf

editorialbot commented 10 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (932.4 files/s, 144123.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             4            140              8           2008
R                               24            175            987           1407
Markdown                         7            224              0            776
XML                              1              0              2            441
TeX                              1              9              0            201
Rmd                              7            199            406            146
YAML                             3             19              6            111
-------------------------------------------------------------------------------
SUM:                            47            766           1409           5090
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 10 months ago

Wordcount for paper.md is 1203

editorialbot commented 10 months ago

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

OK DOIs

- 10.1086/279872 is OK
- 10.1159/000363105 is OK
- 10.1080/10705511.2018.1493385 is OK
- 10/f8rfrg is OK
- 10.1007/s10519-021-10055-x is OK
- 10.1007/s10519-020-10037-5 is OK
- 10/ff3dbm is OK
- 10.1007/s10519-008-9225-0 is OK
- 10.1007/978-0-387-21750-5_5 is OK
- 10.1111/j.2044-8317.1984.tb00802.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 10 months ago

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

osorensen commented 9 months ago

👋 @wjakethompson, @mhu48, could you please update us on how it's going with your reviews?

wjakethompson commented 9 months ago

Sorry for the delay, I'll have mine finished by the end of this week.

mhu48 commented 9 months ago

Review checklist for @mhu48

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 https://github.com/R-Computing-Lab/BGmisc/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@smasongarrison) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[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?

mhu48 commented 9 months ago

Apologies, I generated the list and will start filling in reviews I had from last week.

On Wed, Jan 31, 2024 at 8:44 AM Jake Thompson @.***> wrote:

Sorry for the delay, I'll have mine finished by the end of this week.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6203#issuecomment-1919246193, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKGGVY6MMU3HHOL7ZVTFWRTYRJKD3AVCNFSM6AAAAABBVMM5YCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJZGI2DMMJZGM . You are receiving this because you were mentioned.Message ID: @.***>

wjakethompson commented 9 months ago

Review checklist for @wjakethompson

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 https://github.com/R-Computing-Lab/BGmisc/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@smasongarrison) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[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?

wjakethompson commented 9 months ago

I've complete my review. Just a few notes:

I think installation instruction should include CRAN in addition to GitHub. I opened a PR with a small tweak to the README. crossref: R-Computing-Lab/BGmisc#11
Test coverage is a little low (~63%) and could be better automated. crossref: R-Computing-Lab/BGmisc#12
A few recommendations from goodpractice::gp() to ensure functionality of the package works as intended. crossref: R-Computing-Lab/BGmisc#13

mhu48 commented 9 months ago

I have completed my review. I think overall this is very well-done, but would point out some things to improve.

The software paper needs some improvement in order to make it more accessible to readers who may be not as familiar with the field.
The instructions for installation need to include CRAN, and be made more specific to R.
I second the opinion from @wjakethompson about the automated tests.

smasongarrison commented 9 months ago

The software paper needs some improvement in order to make it more accessible to readers who may be not as familiar with the field.

Thanks! @mhu48 Could you be a little more specific about what information/improvements you'd want to see, as well as clarify which "field" you're referring to? (I just want to make sure that I'm understanding where the gaps are)

smasongarrison commented 9 months ago

@osorensen I've now addressed all the issues raised by the reviewers.

[X] Install instructions for cran are now present #https://github.com/R-Computing-Lab/BGmisc/pull/11
[X] test coverage has been increased from 63% to 85% #https://github.com/R-Computing-Lab/BGmisc/issues/12
[X] code complexity has been reduced to a reasonable range (most complex function is 34, instead of 71) #https://github.com/R-Computing-Lab/BGmisc/issues/13
[X] made the text more accessible to people outside the field of behavior genetics #https://github.com/R-Computing-Lab/BGmisc/issues/20

osorensen commented 9 months ago

Excellent @smasongarrison. @wjakethompson and @mhu48 could you please take a look at these changes and update your review checklists accordingly?

mhu48 commented 8 months ago

Thank you for the updates and the revisions, @smasongarrison. I have reviewed the updated draft and feel that it incorporated significant improvements and sufficiently addressed my concerns from earlier. I have updated the reviewer checklist accordingly. Congratulations!

osorensen commented 8 months ago

Thanks @mhu48!

@smasongarrison, I will now read through the paper a final time and let you know if I have any suggested changes.

osorensen commented 8 months ago

@editorialbot check references

osorensen commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

OK DOIs

- 10.1086/279872 is OK
- 10.1159/000363105 is OK
- 10.1080/10705511.2018.1493385 is OK
- 10/f8rfrg is OK
- 10.1007/s10519-021-10055-x is OK
- 10.1007/s10519-020-10037-5 is OK
- 10/ff3dbm is OK
- 10.1007/s10519-008-9225-0 is OK
- 10.1007/978-0-387-21750-5_5 is OK
- 10.1111/j.2044-8317.1984.tb00802.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 months ago

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

osorensen commented 8 months ago

@smasongarrison I made a PR with a suggested minor change to the paper.

smasongarrison commented 8 months ago

Thanks :) Good catch!

osorensen commented 8 months ago

@editorialbot generate pdf

osorensen commented 8 months ago

@editorialbot commands

editorialbot commented 8 months ago

Hello @osorensen, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for branch
@editorialbot set joss-paper as branch

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@editorialbot set set 10.5281/zenodo.6861996 as archive

# Mention the EiCs for the correct track
@editorialbot ping track-eic

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Flag submission with questionable scope
@editorialbot query scope

# Get a link to the complete list of reviewers
@editorialbot list reviewers

# Creates a post-review checklist with editor and authors tasks
@editorialbot create post-review checklist

# Open the review issue
@editorialbot start review

osorensen commented 8 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[ ] Recommend acceptance with @editorialbot recommend-accept

editorialbot commented 8 months ago

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

osorensen commented 8 months ago

@smasongarrison could you now please do the following?

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[ ] Make sure that the license listed for the archive is the same as the software license.

When done, I can move on with accepting the paper.

smasongarrison commented 8 months ago

@smasongarrison could you now please do the following?

[x] Double check authors and affiliations (including ORCIDs)

[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.

[x] Archive the release on Zenodo/figshare/etc and post the DOI here.

[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

[x] Make sure that the license listed for the archive is the same as the software license.

When done, I can move on with accepting the paper.

smasongarrison commented 8 months ago

@osorensen I think I'm all done :) I was only able to archive on figshare.

Version number in the release is 1.2.0
Archived on figshare at the following DOI: 10.6084/m9.figshare.25238536

osorensen commented 8 months ago

@editorialbot set 1.2.0 as version

editorialbot commented 8 months ago

Done! version is now 1.2.0

osorensen commented 8 months ago

@editorialbot set 10.6084/m9.figshare.25238536 as archive

editorialbot commented 8 months ago

Done! archive is now 10.6084/m9.figshare.25238536

osorensen commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

osorensen commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 8 months ago

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

OK DOIs

- 10.1086/279872 is OK
- 10.1159/000363105 is OK
- 10.1080/10705511.2018.1493385 is OK
- 10/f8rfrg is OK
- 10.1007/s10519-021-10055-x is OK
- 10.1007/s10519-020-10037-5 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10/ff3dbm is OK
- 10.1007/s10519-008-9225-0 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1007/978-0-387-21750-5_5 is OK
- 10.1111/j.2044-8317.1984.tb00802.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value '10/f8rfrg' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.
Element doi: [facet 'pattern'] The value '10/ff3dbm' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

osorensen commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 8 months ago

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

OK DOIs

- 10.1086/279872 is OK
- 10.1159/000363105 is OK
- 10.1080/10705511.2018.1493385 is OK
- 10.1007/s11336-014-9435-8 is OK
- 10.1007/s10519-021-10055-x is OK
- 10.1007/s10519-020-10037-5 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1111/1469-7610.00196 is OK
- 10.1007/s10519-008-9225-0 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1007/978-0-387-21750-5_5 is OK
- 10.1111/j.2044-8317.1984.tb00802.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 months ago

:wave: @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5027, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 8 months ago

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

OK DOIs

- 10.1086/279872 is OK
- 10.1159/000363105 is OK
- 10.1080/10705511.2018.1493385 is OK
- 10.1007/s11336-014-9435-8 is OK
- 10.1007/s10519-021-10055-x is OK
- 10.1007/s10519-020-10037-5 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1111/1469-7610.00196 is OK
- 10.1007/s10519-008-9225-0 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1007/s10519-023-10156-9 is OK
- 10.1007/978-0-387-21750-5_5 is OK
- 10.1111/j.2044-8317.1984.tb00802.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 months ago

:wave: @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5044, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest commented 8 months ago

@editorialbot accept

openjournals / joss-reviews

[REVIEW]: BGmisc: An R Package for Extended Behavior Genetics Analysis #6203

Status

Reviewer instructions & questions

Checklists

Review checklist for @mhu48

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @wjakethompson

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance