editorialbot commented 1 year ago

Submitting author: !--author-handle-->@bernadette-eu@samhforbes<!--end-editor-- Reviewers: @rowlandseymour, @strengejacke Archive: 10.5281/zenodo.8376673

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8ee5ffed37ccbd0a8de519553da6ceea"><img src="https://joss.theoj.org/papers/8ee5ffed37ccbd0a8de519553da6ceea/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8ee5ffed37ccbd0a8de519553da6ceea/status.svg)](https://joss.theoj.org/papers/8ee5ffed37ccbd0a8de519553da6ceea)

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

@rowlandseymour & @strengejacke, 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 @samhforbes 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 @rowlandseymour

📝 Checklist for @strengejacke

editorialbot commented 1 year 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 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (710.4 files/s, 199300.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         7            413              0           7999
C/C++ Header                     2              1             30           2620
XML                              1              0            133           1784
R                               44            497           1818           1726
Rmd                              3            146            356            184
TeX                              1             14              0            101
YAML                             4              5              7             63
C++                              2             14              3             40
-------------------------------------------------------------------------------
SUM:                            64           1090           2347          14517
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1581

editorialbot commented 1 year ago

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

OK DOIs

- 10.48550/arXiv.2211.15229 is OK
- 10.1093/aje/kwt133 is OK
- 10.1371/journal.pcbi.1008409 is OK
- 10.1007/s11222-016-9696-4 is OK
- 10.1038/s41467-021-21237-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

samhforbes commented 1 year ago

Hi @rowlandseymour, @strengejacke and @bernadette-eu this is our review thread. Please feel free to raise and address any issues in the software repository, and then link back to here, or comment here for any wider issues or questions you may have for me.

rowlandseymour commented 1 year ago

Review checklist for @rowlandseymour

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/bernadette-eu/Bernadette?
[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 (@bernadette-eu) 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?

rowlandseymour commented 1 year ago

@samhforbes Thanks for starting the review thread, Sam. I found this to be a substantial and well presented package. I spent yesterday playing around with it and trying to break various parts. There are lots of nice error messages and automated tests. From what I can see, it is implementing the Bayesian hierarchal model it is supposed to. The paper sets out the rationale and background, though I think the summary could be improved. There are comments throughout the repository. I've raised a couple of minor issues, and when these are done, I'm happy to recommend it be accepted.

strengejacke commented 1 year ago

Review checklist for @strengejacke

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/bernadette-eu/Bernadette?
[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 (@bernadette-eu) 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?

bernadette-eu commented 1 year ago

Thank you @rowlandseymour for your feedback.

I am currently working to address your comments. @samhforbes I was wondering about good practices when dealing with these open issues/ reviewer comments on Github. Is it more preferable to create a PR (i.e. "joss_reviews") perform the changes and then merge with master? Or work directly on the master branch? Looking at other JOSS issues/reviews, I can see the former happening.

@rowlandseymour I will let you know if I have any follow-up clarifications.

Lampros Bouranis

samhforbes commented 1 year ago

Hi @bernadette-eu this is up to your personal workflow preferences - we see both examples.

bernadette-eu commented 1 year ago

@rowlandseymour

Thank you for your support on this work. I have addressed your comments and have replied at each issue that you have opened. Happy to address your comments further, if my responses are not satisfactory.

All the best, Lampros Bouranis

rowlandseymour commented 1 year ago

@bernadette-eu Thanks for addressing all of those comments. I should have said earlier, it's a nice package, I think you must have put a lot of work into this.

@samhforbes My review is now complete and I'm happy to recommend accepting this.

bernadette-eu commented 1 year ago

@rowlandseymour Thank you for your informative review. It's actually a 2-year effort, during the MSCA Fellowship ! :)

samhforbes commented 1 year ago

Hi @strengejacke I hope all is well! Please let me know if you need anything further to complete your review.

bernadette-eu commented 1 year ago

Hi @samhforbes hope you had a great summer break! I see that strengejacke has already completed most of the review and wanted to check for a progress update on that (given that things are slower during the summer). Happy to address any comments from the reviewer.

All the best, Lampros Bouranis

strengejacke commented 1 year ago

Sorry for being quiet the past time, because I was busy first and then on vacation. I will get back to the remaining part of the review tomorrow.

bernadette-eu commented 1 year ago

Hi @strengejacke hope you are doing well! Just checking in regarding the completion of the review. If you need anything further, do let me know.

Thanks, Lampros

samhforbes commented 1 year ago

Hi @strengejacke we look forward to the remainder of your review. Please let us know if there will be any issue getting this done soon.

strengejacke commented 1 year ago

Thanks, one minor issue and one recommendation to be addressed.

bernadette-eu commented 1 year ago

@strengejacke

Thank you for your feedback. I have addressed your comments and have replied at each issue that you have opened. Happy to address your comments further, if my responses are not satisfactory.

All the best, Lampros Bouranis

strengejacke commented 1 year ago

Thanks, @samhforbes I recommend accept! Sorry for the huge delay in reviewing the paper...

samhforbes commented 1 year ago

Fabulous, thank you both @rowlandseymour and @strengejacke

samhforbes commented 1 year ago

@bernadette-eu I am going to now begin the post-review stage, so there are a few things for you to do alongside the final checks I need to do. This is a nice package, well done!

samhforbes commented 1 year ago

@editorialbot make post-review checklist

editorialbot commented 1 year ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

samhforbes commented 1 year ago

@editorialbot commands

editorialbot commented 1 year ago

Hello @samhforbes, 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

samhforbes commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[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.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[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
[x] Recommend acceptance with @editorialbot recommend-accept

samhforbes commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

bernadette-eu commented 1 year ago

@bernadette-eu I am going to now begin the post-review stage, so there are a few things for you to do alongside the final checks I need to do. This is a nice package, well done!

Hi @samhforbes ,

All changes were made in the joss_review branch. Let me merge with the master branch first and we'll generate the pdf again.

Thanks, Lampros Bouranis

samhforbes commented 1 year ago

Oh - thanks, sorry I missed that. If you haven't already, please check the capitalisation of references in the paper (I see Cori et al for example is all capitalised in the title, whereas others are not).

bernadette-eu commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

bernadette-eu commented 1 year ago

@samhforbes below is the information on the Zenodo DOI and release version of the software for you. I think the "Additional Author Tasks After Review is Complete" list checks out - please let me know if I can provide further information. You can proceed by generating the pdf.

Version Number: v1.1.5 DOI: https://doi.org/10.5281/zenodo.8376673

samhforbes commented 1 year ago

@editorialbot set v1.1.5 as version

editorialbot commented 1 year ago

Done! version is now v1.1.5

samhforbes commented 1 year ago

@editorialbot set https://doi.org/10.5281/zenodo.8376673 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8376673

samhforbes commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.48550/arXiv.2211.15229 is OK
- 10.1093/aje/kwt133 is OK
- 10.1371/journal.pcbi.1008409 is OK
- 10.1007/s11222-016-9696-4 is OK
- 10.1038/s41467-021-21237-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

samhforbes commented 1 year ago

Hi @bernadette-eu please add

the DOI for Carpenter et al (I think https://doi.org/10.18637/jss.v076.i01 is right)
Volume and pages for Cori et al 2013

bernadette-eu commented 1 year ago

the DOI for Carpenter et al (I think https://doi.org/10.18637/jss.v076.i01 is right)

Yeap, this this the correct one.

Volume and pages for Cori et al 2013

I have fixed that reference.

bernadette-eu commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

bernadette-eu commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

bernadette-eu commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.48550/arXiv.2211.15229 is OK
- 10.18637/jss.v076.i01 is OK
- 10.1093/aje/kwt133 is OK
- 10.1371/journal.pcbi.1008409 is OK
- 10.1007/s11222-016-9696-4 is OK
- 10.1038/s41467-021-21237-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

openjournals / joss-reviews

[REVIEW]: Bernadette: Bayesian Inference and Model Selection for Stochastic Epidemics in R #5612

Status

Reviewer instructions & questions

Checklists

Review checklist for @rowlandseymour

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @strengejacke

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