[REVIEW]: individual: An R package for individual-based epidemiological models

whedon commented 3 years ago

Submitting author: @giovannic (Giovanni Charles) Repository: https://github.com/mrc-ide/individual Version: v0.1.6 Editor: @mikldk Reviewer: @seabbs, @strengejacke, @SteRoe Archive: 10.5281/zenodo.5529932

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Reviewer instructions & questions

@seabbs & @strengejacke & @SteRoe, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

Conflict of interest

[ ] 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

[ ] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[ ] Repository: Is the source code for this software available at the repository url?
[ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@giovannic) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

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

[ ] 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.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] 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?
[ ] 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

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] 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 and who the target audience is?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] 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?

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 repository url?
[x] #3591
[x] Contribution and authorship: Has the submitting author (@giovannic) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @SteRoe

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 (@giovannic) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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whedon commented 3 years ago

Wordcount for paper.md is 1188

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (1013.5 files/s, 118558.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               24            374            381           1782
C++                             13            149            229           1657
C/C++ Header                    12            204            128            997
TeX                              1             42              0            441
Markdown                         3             61              0            233
Rmd                              4            152            243            214
YAML                             5             32              2            150
Dockerfile                       1              4              1              9
Bourne Shell                     1              0              0              2
-------------------------------------------------------------------------------
SUM:                            64           1018            984           5485
-------------------------------------------------------------------------------

Statistical information for the repository 'c99a2ebcc471e80da37242e7' was
gathered on 2021/07/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Giovanni                        21          1106            738           11.83
Giovanni Charles                62          6408           4758           71.66
Peter Winskill                   1            36              0            0.23
giovanni                         3           280            198            3.07
slwu89                          41          1637            421           13.21

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Giovanni                   2218          200.5          8.4               10.96
slwu89                     1146           70.0          3.9               10.82

whedon commented 3 years ago

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

OK DOIs

- 10.1007/978-0-387-33532-2_2 is OK
- 10.1186/1471-2334-10-190 is OK
- 10.1186/s12879-017-2699-8 is OK
- 10.1146/annurev-publhealth-040617-014317 is OK
- 10.1146/annurev-statistics-010814-020218 is OK
- 10.1146/annurev-statistics-061120-034438 is OK
- 10.1016/j.tree.2012.01.014 is OK
- 10.18637/jss.v040.i08 is OK
- 10.1186/1471-2105-13-76 is OK
- 10.1186/2194-3206-1-3 is OK
- 10.25080/majora-7b98e3ed-009 is OK
- 10.18637/jss.v090.i02 is OK
- 10.5281/zenodo.4441210 is OK
- 10.1111/ecog.04516 is OK
- 10.1111/2041-210X.13286 is OK
- 10.1016/j.epidem.2018.06.001 is OK
- 10.1016/j.procs.2013.05.347 is OK
- 10.18637/jss.v058.i02 is OK
- 10.1093/femspd/fty059 is OK
- 10.1101/440834 is OK
- 10.1177/1094342016635723 is OK
- 10.18637/jss.v094.i06 is OK
- 10.1002/ece3.2580 is OK
- 10.18637/jss.v022.i09 is OK
- 10.18637/jss.v084.i08 is OK
- 10.18637/jss.v083.i11 is OK
- 10.18637/jss.v024.i02 is OK
- 10.1111/2041-210X.13422 is OK
- 10.1109/tcss.2018.2871625 is OK
- 10.1016/j.idm.2017.03.001 is OK
- 10.1101/2021.05.13.21256216 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

mikldk commented 3 years ago

@seabbs, @strengejacke, @SteRoe: Thanks for agreeing to review. Please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

SteRoe commented 3 years ago

@mikldk: This is my first JOSS review. Filled out the check list, but I'm not sure how to submit it. Most notably I found no statement on examples and tests, so I left these checks open. Other points are fine. How to proceed?

mikldk commented 3 years ago

@SteRoe Thanks for asking! The check items are not to be submitted, once they are checked that is saved and all is good. The ones you do not think are okay/not satisfied you can address here in this issue to the author (minor things), or preferably create issues in the submission's repository and mention this review issue so that the issues are linked.

giovannic commented 3 years ago

@mikldk @SteRoe Thanks for bringing that up! Not sure how we declare these to JOSS but we have extensive automated tests (here's our latest coverage), and our documentation has an example in the tutorial (which had to be removed from the paper for brevity).

giovannic commented 3 years ago

Some other potentially useful links...

Installation instructions Contributing guidelines

;)

SteRoe commented 3 years ago

@giovannic Maybe, you could reference your test suite and the tutorial in a short section?

giovannic commented 3 years ago

I've added a short note to the Licensing and Availability section.

whedon commented 3 years ago

:wave: @SteRoe, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @seabbs, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @strengejacke, please update us on how your review is going (this is an automated reminder).

mikldk commented 3 years ago

@seabbs, @strengejacke, @SteRoe: Can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

SteRoe commented 3 years ago

My points were properly replied. For me, the manuscript is fine. How to proceed?

mikldk commented 3 years ago

@SteRoe Your checklist at the top is still not entirely completed. Please go through all items and either verify the item is satisfactory by checking it, or raise an issue (here or as a dedicated issue in the repository). When you are done please let me know. Please don't close this issue; the system will do that automatically when the review is finished.

SteRoe commented 3 years ago

o.k., thanks @mikldk: I've completed my checklist and I'm fine with the manuscript.

strengejacke commented 3 years ago

I completed my review. I raised some issues, which were addressed to my satisfaction. Hence, from my side, I would recommend accept.

mikldk commented 3 years ago

@seabbs, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

slwu89 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:

mikldk commented 3 years ago

@seabbs , can you please give a status of your review?

mikldk commented 2 years ago

@seabbs Please respond before Sep 22 or else I will have to find another reviewer. (I have also tried to reach you multiple times by mail, including now.)

slwu89 commented 2 years ago

@mikldk would you like me to look over the list of potential reviewers again to suggest another alternative person? Or would it be appropriate to publish with 2 reviewers? I'm also interested in getting this review wrapped up as soon as possible. Thanks for your help editing our submission!

mikldk commented 2 years ago

@slwu89 Unfortunately @seabbs is unresponsive, but we will proceed as two other reviewers already reviewed the paper.

Please have a final read though of the paper, checking language etc.
Have a final check of the proofs with @whedon generate pdf
In general, be sure that all versions are correct and that the repo is in the state that should be published.
Please make a tagged release and archive (e.g. with Zenodo) as described here, and report the version number and archive DOI in this thread. Please verify that the archive deposit has the correct metadata (title and author list), or edit these if that is not the case.

giovannic commented 2 years ago

Thanks @mikldk ,

We've published v1.6 here, with DOI: 10.5281/zenodo.5529932

Will do a final check of the paper...

@whedon generate pdf

slwu89 commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

slwu89 commented 2 years ago

Hi @mikldk, we've finished checking the proofs of the paper. Everything seems to be in order.

mikldk commented 2 years ago

@whedon set 10.5281/zenodo.5529932 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5529932 is the archive.

mikldk commented 2 years ago

@whedon set v1.6 as version

whedon commented 2 years ago

OK. v1.6 is the version.

mikldk commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

mikldk commented 2 years ago

@slwu89 @giovannic: At Zenodo you write v1.6 (right hand sidebar), but the release at Github is v0.1.6 (from Aug 20?)? Also, the names on the paper and at Zenodo do not match, please make consistent.

giovannic commented 2 years ago

@mikldk Done, thanks

mikldk commented 2 years ago

@whedon set v0.1.6 as version

whedon commented 2 years ago

OK. v0.1.6 is the version.

mikldk commented 2 years ago

@giovannic Middle initial missing from Zenodo?

giovannic commented 2 years ago

@mikldk Ah, ok done 👍

mikldk commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

mikldk commented 2 years ago

@giovannic:

In the Summary section, you write "individual based models (IBMs)" - would it be appropriate to also include the term "agent based models (ABM)"?
Sometimes you write "individual based" and others "individual-based". Please use the same form.
"General R Packages" vs "Design Principles" vs "State of the field" - please either use Title Case consistently, or don't use it :smile:.
Acknowledgements: Please end the section with a period. Also, please write what you acknowledge them for.

giovannic commented 2 years ago

👍 done

giovannic commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

mikldk commented 2 years ago

@giovannic The title still says "[...] for individual based epidemiological models" - without hyphen?

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