[REVIEW]: EoN (Epidemics on Networks), software for simulation, analytic approximation, and analysis of epidemics on networks

whedon commented 4 years ago

Submitting author: @joelmiller (Joel Miller) Repository: https://github.com/springer-math/Mathematics-of-Epidemics-on-Networks Version: v1.1 Editor: @lpantano Reviewers: @acolum, @pholme, @hagberg Archive: 10.5281/zenodo.3572756

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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

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

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Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @acolum

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 (@joelmiller) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @pholme

Conflict of interest

[ ] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 (@joelmiller) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @hagberg

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 (@joelmiller) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 4 years ago

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

: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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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

@whedon commands

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

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

acolum commented 4 years ago

Just finished my review - everything looks great!

lpantano commented 4 years ago

Thank you @acolum! 👋 @pholme let me know if you need something else to complete the review.

lpantano commented 4 years ago

👋 @pholme, are you still able to review this? Let me know.

lpantano commented 4 years ago

@whedon add @hagberg as reviewer

whedon commented 4 years ago

OK, @hagberg is now a reviewer

lpantano commented 4 years ago

@hagberg how is the review going?

lpantano commented 4 years ago

Hi @hagberg, did you end up opening the issues to ask the authors to change issues you saw during the review? If yes, can you link them here? Thanks!

joelmiller commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

PDF failed to compile for issue #1731 with the following error:

Error reading bibliography ./paper.bib (line 39, column 1): unexpected "y" expecting space, ",", white space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

joelmiller commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

joelmiller commented 4 years ago

Hi @lpantano - Do you know if there is any way to embed a video into the pdf file? One of the final things I want to show is a tool to build an animation, but at present I can't find any way to embed it.

joelmiller commented 4 years ago

@hagberg

I've added the functional testing (created by @tinghf ) into the repository under EoN/tests

I've also added a discussion of related packages into the paper.

Let me know of anything else you'd like improved.

hagberg commented 4 years ago

Looks good. Issues are closed.

joelmiller commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

lpantano commented 4 years ago

Hi @lpantano - Do you know if there is any way to embed a video into the pdf file? One of the final things I want to show is a tool to build an animation, but at present I can't find any way to embed it.

I will need to ask about this, not sure this is possible.

danielskatz commented 4 years ago

I’m fairly sure the answer is no

joelmiller commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

joelmiller commented 4 years ago

@lpantano @danielskatz

Okay - I've removed the animation from the paper.md file. Should be good to go now.

lpantano commented 4 years ago

@whedon check references

whedon commented 4 years ago

Attempting to check references...

whedon commented 4 years ago


OK DOIs

- 10.1098/rsif.2011.0403 is OK
- 10.1103/PhysRevE.80.020901 is OK
- 10.6084/m9.figshare.1164194 is OK

MISSING DOIs

- https://doi.org/10.1016/j.cpc.2017.06.007 may be missing for title: Optimized Gillespie algorithms for the simulation of Markovian epidemic processes on large and heterogeneous networks
- https://doi.org/10.1090/s0002-9947-1945-0013857-4 may be missing for title: Markoff chains–denumerable case
- https://doi.org/10.18637/jss.v084.i08 may be missing for title: EpiModel: An R Package for Mathematical  Modeling of Infectious Disease over Networks
- https://doi.org/10.1093/comnet/cnv021 may be missing for title: Complex contagions and hybrid phase transitions
- https://doi.org/10.1101/297267 may be missing for title: FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences
- https://doi.org/10.1186/s13362-019-0058-7 may be missing for title: A monotonic relationship between the variability of the infectious period and final size in pairwise epidemic modelling
- https://doi.org/10.1515/9781400841356.497 may be missing for title: A simple model of global cascades on random networks
- https://doi.org/10.1086/jar.33.4.3629752 may be missing for title: An information flow model for conflict and fission in small groups

INVALID DOIs

- None

lpantano commented 4 years ago

@joelmiller, it seems there are missing DOIs, can you double check this? Thanks!

joelmiller commented 4 years ago

@whedon check references

whedon commented 4 years ago

Attempting to check references...

whedon commented 4 years ago


OK DOIs

- 10.1016/j.physa.2006.06.018 is OK
- 10.1016/j.cpc.2017.06.007 is OK
- 10.1090/S0002-9947-1945-0013857-4 is OK
- 10.18637/jss.v084.i08 is OK
- 10.1007/978-3-319-50806-1 is OK
- 10.1021/j100540a008 is OK
- 10.25080/issn.2575-9752 is OK
- 10.1093/comnet/cnv021 is OK
- 10.1098/rsif.2011.0403 is OK
- 10.1103/PhysRevE.80.020901 is OK
- 10.1093/bioinformatics/bty921 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1103/PhysRevLett.103.058701 is OK
- 10.1186/s13362-019-0058-7 is OK
- 10.1073/pnas.082090499 is OK
- 10.1086/jar.33.4.3629752 is OK

MISSING DOIs

- None

INVALID DOIs

- None

joelmiller commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

joelmiller commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

joelmiller commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

joelmiller commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

joelmiller commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

openjournals / joss-reviews