[REVIEW]: EoN (Epidemics on Networks), software for simulation, analytic approximation, and analysis of epidemics on networks #1731

whedon · 2019-09-15T03:14:02Z

Submitting author: @joelmiller (Joel Miller)
Repository: https://github.com/springer-math/Mathematics-of-Epidemics-on-Networks
Version: v1.0.8
Editor: @lpantano
Reviewers: @acolum, @pholme, @hagberg
Archive: Pending

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

Review checklist for @acolum

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 @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

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?

whedon · 2019-09-15T03:14:05Z

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 🎉.

⭐️ 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:

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

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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 · 2019-09-15T03:14:06Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-09-15T03:14:42Z

👉 Check article proof 📄 👈

acolum · 2019-09-24T21:55:54Z

Just finished my review - everything looks great!

lpantano · 2019-10-03T13:21:53Z

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

lpantano · 2019-10-18T11:48:45Z

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

lpantano · 2019-10-23T17:12:23Z

@whedon add @hagberg as reviewer

whedon · 2019-10-23T17:12:30Z

OK, @hagberg is now a reviewer

lpantano · 2019-11-11T14:27:11Z

@hagberg how is the review going?

lpantano · 2019-11-25T14:54:37Z

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 · 2019-12-03T22:53:39Z

@whedon generate pdf

whedon · 2019-12-03T22:53:41Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-03T22:53:54Z

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 · 2019-12-03T22:58:56Z

@whedon generate pdf

whedon · 2019-12-03T22:58:59Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-03T22:59:28Z

👉 Check article proof 📄 👈

joelmiller · 2019-12-03T23:30:23Z

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 · 2019-12-04T09:58:30Z

@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 · 2019-12-05T22:41:00Z

Looks good. Issues are closed.

whedon · 2019-12-06T20:19:44Z


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 · 2019-12-06T20:38:48Z

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

joelmiller · 2019-12-09T03:41:31Z

@whedon check references

whedon · 2019-12-09T03:41:34Z

Attempting to check references...

whedon · 2019-12-09T03:41:54Z


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 · 2019-12-09T03:45:03Z

@whedon generate pdf

whedon · 2019-12-09T03:45:06Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-09T03:45:37Z

👉 Check article proof 📄 👈

joelmiller · 2019-12-09T04:15:18Z

@whedon generate pdf

whedon · 2019-12-09T04:15:21Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-09T04:15:50Z

👉 Check article proof 📄 👈

joelmiller · 2019-12-09T04:26:04Z

@whedon generate pdf

whedon · 2019-12-09T04:26:07Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-09T04:26:35Z

👉 Check article proof 📄 👈

joelmiller · 2019-12-09T04:30:07Z

@whedon generate pdf

whedon · 2019-12-09T04:30:10Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-09T04:31:07Z

👉 Check article proof 📄 👈

joelmiller · 2019-12-10T01:51:36Z

@whedon generate pdf

whedon · 2019-12-10T01:51:39Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-10T01:52:22Z

👉 Check article proof 📄 👈

joelmiller · 2019-12-10T02:02:20Z

@whedon generate pdf

whedon · 2019-12-10T02:02:23Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-10T02:03:08Z

👉 Check article proof 📄 👈

joelmiller · 2019-12-10T02:03:12Z

@whedon check references

whedon · 2019-12-10T02:03:15Z

Attempting to check references...

whedon · 2019-12-10T02:03:36Z


OK DOIs

- 10.1016/j.physa.2006.06.018 is OK
- 10.1016/j.cpc.2017.06.007 is OK
- 10.1103/PhysRevE.96.022301 is OK
- 10.1090/S0002-9947-1945-0013857-4 is OK
- 10.18637/jss.v084.i08 is OK
- 10.1021/j100540a008 is OK
- 10.1103/PhysRevE.93.042316 is OK
- 10.25080/issn.2575-9752 is OK
- 10.1007/978-3-319-50806-1 is OK
- 10.1063/1.5010002 is OK
- 10.1103/PhysRevE.87.060801 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 · 2019-12-10T02:07:24Z

@lpantano - I think this is good to go now. I've updated the references and gone through the paper a couple times.

lpantano · 2019-12-10T03:23:28Z

thank you! Last step is to create a Zenodo archive: The title needs to be the same than in the paper, together with the authors. When you are ready you can paste here the Zenodo link. Thanks!

joelmiller · 2019-12-10T03:55:06Z

@lpantano

That's actually a bit problematic. The software was developed initially alongside a textbook I was writing, so it sits within https://github.com/springer-math (which I don't own). I've sent a request to give Zenodo the necessary access. But the editor who set up that site has left the company, and I'm not even sure that anyone will get the message. It looks like it hasn't been used since he left (over a year ago).

Thoughts? The obvious idea would be to create a new repository. But I prefer to move things around as little as possible.

danielskatz · 2019-12-10T12:56:40Z

You can simply tar the repo and manually deposit it in Zenodo (or figshare, or any other archival repository that will accept it and provide a DOI)

This is what the GitHub - Zenodo link automates, but you don't have to use the automatic mechanism

whedon added the review label Sep 15, 2019

whedon assigned lpantano Sep 15, 2019

whedon mentioned this issue Sep 15, 2019

[PRE REVIEW]: EoN (Epidemics on Networks), software for simulation, analytic approximation, and analysis of epidemics on networks #1673

Closed

whedon assigned acolum Sep 16, 2019

whedon assigned acolum and lpantano and unassigned lpantano and acolum Oct 23, 2019

whedon assigned hagberg Oct 25, 2019

This was referenced Nov 26, 2019

Functional testing springer-math/Mathematics-of-Epidemics-on-Networks#43

Closed

Adding related work and refs to paper springer-math/Mathematics-of-Epidemics-on-Networks#44

Closed

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[REVIEW]: EoN (Epidemics on Networks), software for simulation, analytic approximation, and analysis of epidemics on networks #1731

[REVIEW]: EoN (Epidemics on Networks), software for simulation, analytic approximation, and analysis of epidemics on networks #1731

Comments

whedon commented Sep 15, 2019 • edited by hagberg

Status

Reviewer instructions & questions

Review checklist for @acolum

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @pholme

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @hagberg

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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edited by hagberg