[REVIEW]: individual: An R package for individual-based epidemiological models #3539

whedon · 2021-07-26T08:40:36Z

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

⚠️ JOSS reduced service mode ⚠️

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Markdown: [![status](https://joss.theoj.org/papers/78bcf904694df41cd9a722d0165cd2ad/status.svg)](https://joss.theoj.org/papers/78bcf904694df41cd9a722d0165cd2ad)

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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

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? #3591
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 @SteRoe

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?

The text was updated successfully, but these errors were encountered:

whedon · 2021-07-26T08:40:40Z

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 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

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

@whedon generate pdf

whedon · 2021-07-26T08:40:45Z

Wordcount for paper.md is 1188

whedon · 2021-07-26T08:40:47Z

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 · 2021-07-26T08:40:55Z

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 · 2021-07-26T08:41:12Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

mikldk · 2021-07-26T08:44:46Z

@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 · 2021-07-26T10:37:29Z

@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 · 2021-07-26T10:53:18Z

@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 · 2021-07-26T14:58:47Z

@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 · 2021-07-26T15:03:23Z

Some other potentially useful links...

Installation instructions
Contributing guidelines

;)

SteRoe · 2021-07-26T15:22:24Z

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

giovannic · 2021-07-27T09:40:54Z

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

whedon · 2021-08-09T08:40:46Z

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

whedon · 2021-08-09T08:40:46Z

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

whedon · 2021-08-09T08:40:46Z

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

mikldk · 2021-08-23T07:03:45Z

@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 · 2021-08-23T09:38:01Z

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

giovannic · 2021-10-05T08:29:00Z

@mikldk Ah, ok done 👍

mikldk · 2021-10-05T08:53:56Z

@whedon generate pdf

whedon · 2021-10-05T08:54:25Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

mikldk · 2021-10-05T09:55:20Z

@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 😄.
Acknowledgements: Please end the section with a period. Also, please write what you acknowledge them for.

giovannic · 2021-10-05T14:21:53Z

👍 done

giovannic · 2021-10-05T14:22:06Z

@whedon generate pdf

whedon · 2021-10-05T14:22:49Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

mikldk · 2021-10-05T17:51:15Z

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

slwu89 · 2021-10-05T17:54:03Z

@mikldk I've addressed that here mrc-ide/individual@ec4f1be

slwu89 · 2021-10-05T17:54:12Z

@whedon generate pdf

whedon · 2021-10-05T17:54:38Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

mikldk · 2021-10-05T18:08:02Z

@whedon recommend-accept

whedon · 2021-10-05T18:08:06Z

Attempting dry run of processing paper acceptance...

whedon · 2021-10-05T18:08:20Z

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 · 2021-10-05T18:08:39Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2645

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2645, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

mikldk · 2021-10-05T18:09:34Z

@openjournals/joss-eics : Please note that the title has changed (a hyphen added to "individual-based"). I changed the issue title here, but I am not sure if it needs to be changed elsewhere, too.

kyleniemeyer · 2021-10-07T16:00:41Z

@openjournals/dev does the title need to be changed anywhere else, or will it be fine if correct in the paper?

kyleniemeyer · 2021-10-07T16:03:01Z

I'm going to proceed assuming that is the case, since the generated XML and PDF are correct.

kyleniemeyer · 2021-10-07T16:03:29Z

@whedon accept deposit=true

whedon · 2021-10-07T16:03:33Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2021-10-07T16:04:09Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-10-07T16:04:10Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03539 joss-papers#2651
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03539
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2021-10-07T16:08:30Z

Congratulations @giovannic on your article's publication in JOSS!

Many thanks to @strengejacke and @SteRoe for reviewing this, and @mikldk for editing it.

whedon · 2021-10-07T16:08:33Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03539/status.svg)](https://doi.org/10.21105/joss.03539)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03539">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03539/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03539/status.svg
   :target: https://doi.org/10.21105/joss.03539

This is how it will look in your documentation:

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slwu89 · 2021-10-07T16:12:53Z

Thank you @SteRoe and @strengejacke for reviewing our paper, and to @mikldk for editing our submission!

whedon added C C++ R review labels Jul 26, 2021

whedon assigned mikldk Jul 26, 2021

whedon mentioned this issue Jul 26, 2021

[PRE REVIEW]: individual: An R package for individual based epidemiological models #3377

Closed

whedon assigned seabbs, SteRoe and strengejacke Jul 27, 2021

slwu89 mentioned this issue Jul 27, 2021

add badges for coverage and R CMD CHECK to readme mrc-ide/individual#128

Merged

This was referenced Aug 9, 2021

[JOSS] plain LICENSE file not showing OSI conform text mrc-ide/individual#132

Closed

[JOSS] Statement of need mrc-ide/individual#133

Closed

SteRoe closed this as completed Aug 23, 2021

mikldk changed the title ~~[REVIEW]: individual: An R package for individual based epidemiological models~~ [REVIEW]: individual: An R package for individual-based epidemiological models Oct 5, 2021

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 5, 2021

whedon added accepted published Papers published in JOSS labels Oct 7, 2021

kyleniemeyer closed this as completed Oct 7, 2021

[REVIEW]: individual: An R package for individual-based epidemiological models #3539

[REVIEW]: individual: An R package for individual-based epidemiological models #3539

Comments

whedon commented Jul 26, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @seabbs

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

Review checklist for @SteRoe

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Jul 26, 2021

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mikldk commented Jul 26, 2021

SteRoe commented Jul 26, 2021

mikldk commented Jul 26, 2021

giovannic commented Jul 26, 2021

giovannic commented Jul 26, 2021

SteRoe commented Jul 26, 2021

giovannic commented Jul 27, 2021

whedon commented Aug 9, 2021

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mikldk commented Aug 23, 2021

SteRoe commented Aug 23, 2021

giovannic commented Oct 5, 2021

mikldk commented Oct 5, 2021

whedon commented Oct 5, 2021

mikldk commented Oct 5, 2021

giovannic commented Oct 5, 2021

giovannic commented Oct 5, 2021

whedon commented Oct 5, 2021

mikldk commented Oct 5, 2021

slwu89 commented Oct 5, 2021

slwu89 commented Oct 5, 2021

whedon commented Oct 5, 2021

mikldk commented Oct 5, 2021

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mikldk commented Oct 5, 2021

kyleniemeyer commented Oct 7, 2021

kyleniemeyer commented Oct 7, 2021

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whedon commented Oct 7, 2021

whedon commented Oct 7, 2021

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kyleniemeyer commented Oct 7, 2021

whedon commented Oct 7, 2021

slwu89 commented Oct 7, 2021

whedon commented Jul 26, 2021 •

edited

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