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[PRE REVIEW]: PAM: Population Activity Modeller #5845

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editorialbot opened this issue Sep 13, 2023 · 68 comments
Closed

[PRE REVIEW]: PAM: Population Activity Modeller #5845

editorialbot opened this issue Sep 13, 2023 · 68 comments
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@jamesdamillington @martibosch @martinfleis
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Dockerfile pre-review Python TeX Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences

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editorialbot commented Sep 13, 2023 •
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Submitting author: @fredshone (Fred Shone)
Repository: https://github.com/arup-group/pam
Branch with paper.md (empty if default branch): joss
Version: v0.2.4
Editor: @martinfleis
Reviewers: @jamesdamillington, @martibosch
Managing EiC: Olivia Guest

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status

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HTML: <a href="https://joss.theoj.org/papers/c8737f0649d60fffcd3ba0aa25fa5f40"><img src="https://joss.theoj.org/papers/c8737f0649d60fffcd3ba0aa25fa5f40/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c8737f0649d60fffcd3ba0aa25fa5f40/status.svg)](https://joss.theoj.org/papers/c8737f0649d60fffcd3ba0aa25fa5f40)

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Thanks for submitting your paper to JOSS @fredshone. Currently, there isn't a JOSS editor assigned to your paper.

@fredshone if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences labels Sep 13, 2023
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Hello human, 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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.29 s (652.1 files/s, 201482.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         103           4789           2487          18491
JSON                             5              0              0           4770
XML                             17            182             39           4143
Jupyter Notebook                18              0          17653           2387
Markdown                        16            306              0            753
YAML                            14             37              8            478
SQL                              3              0              0            164
XSD                              1              8              2            125
DTD                              4             89            254            102
TOML                             1             24             14             82
TeX                              1              5              0             43
HTML                             1              3              1              9
CSS                              1              1              2              7
Dockerfile                       1              2              0              7
-------------------------------------------------------------------------------
SUM:                           186           5446          20460          31561
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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

OK DOIs

- 10.14279/depositonce-9835 is OK

MISSING DOIs

- 10.17226/22357 may be a valid DOI for title: Activity-Based Travel Demand Models: A Primer
- 10.1080/12265934.2013.835118 may be a valid DOI for title: Activity-based models of travel demand: promises, progress and prospects

INVALID DOIs

- None

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Wordcount for paper.md is 540

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

@oliviaguest
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Hey, thanks for submitting to JOSS, @fredshone. I am going to try and find an editor for you, but can you also check the missing refs while I do that, please? Thanks!

@oliviaguest
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hi @martinfleis is this up your street and do you have capacity?

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Hello @fredshone, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# 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 branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

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@editorialbot check references

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

OK DOIs

- 10.5334/baw is OK
- 10.17226/22357 is OK
- 10.1080/12265934.2013.835118 is OK
- 10.14279/depositonce-9835 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@arfon
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arfon commented Sep 27, 2023

@editorialbot generate pdf

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arfon commented Sep 27, 2023

@editorialbot invite @martinfleis as editor

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Invitation to edit this submission sent!

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

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Five most similar historical JOSS papers:

pyam: a Python Package for the Analysis and Visualization of Models of the Interaction of Climate, Human, and Environmental Systems
Submitting author: @gidden
Handling editor: @lheagy (Retired)
Reviewers: @jtmiclat, @Chilipp
Similarity score: 0.8160

Melodie: Agent-based Modeling in Python
Submitting author: @SongminYu
Handling editor: @jbytecode (Active)
Reviewers: @JoelForamitti, @rusu24edward
Similarity score: 0.8105

pymdp: A Python library for active inference in discrete state spaces
Submitting author: @conorheins
Handling editor: @emdupre (Active)
Reviewers: @seankmartin, @patrickmineault
Similarity score: 0.8091

Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle
Submitting author: @barneydobson
Handling editor: @crvernon (Active)
Reviewers: @cheginit, @jlarsen-usgs
Similarity score: 0.8068

LoadProfileGenerator: An Agent-Based Behavior Simulation for Generating Residential Load Profiles
Submitting author: @noah80
Handling editor: @fraukewiese (Active)
Reviewers: @mewilhel, @szkafander
Similarity score: 0.8068

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

@martinfleis
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@editorialbot add me as editor

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Assigned! @martinfleis is now the editor

@martinfleis
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Hi @fredshone 👋, I'll be the editor if this submission. If you'll have any queries, send them my way.

If you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission. Your submission is slightly off my expertise, so any help with finding suitable reviewers would help. Thanks!

@martinfleis
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@editorialbot generate pdf

@martinfleis
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@editorialbot check references

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

OK DOIs

- 10.5334/baw is OK
- 10.17226/22357 is OK
- 10.1080/12265934.2013.835118 is OK
- 10.14279/depositonce-9835 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@editorialbot
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Five most similar historical JOSS papers:

AgentPy: A package for agent-based modeling in Python
Submitting author: @JoelForamitti
Handling editor: @sbenthall (Active)
Reviewers: @jamesdamillington, @martibosch
Similarity score: 0.8164

Melodie: Agent-based Modeling in Python
Submitting author: @SongminYu
Handling editor: @jbytecode (Active)
Reviewers: @JoelForamitti, @rusu24edward
Similarity score: 0.8117

pymdp: A Python library for active inference in discrete state spaces
Submitting author: @conorheins
Handling editor: @emdupre (Active)
Reviewers: @seankmartin, @patrickmineault
Similarity score: 0.8097

LoadProfileGenerator: An Agent-Based Behavior Simulation for Generating Residential Load Profiles
Submitting author: @noah80
Handling editor: @fraukewiese (Active)
Reviewers: @mewilhel, @szkafander
Similarity score: 0.8059

Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle
Submitting author: @barneydobson
Handling editor: @crvernon (Active)
Reviewers: @cheginit, @jlarsen-usgs
Similarity score: 0.8059

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

@fredshone
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@martinfleis ready for review again.

Following your feedback I have added two new sections:

  • Existing tools review (reviews existing relevant open tools we are aware of)
  • Design (high level description of how project works)

Many thanks for your time.

@martinfleis
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Hi @jofmi and @SongminYu, you have recently published JOSS papers in a similar domain as this submission. Would you be willing to take the role of a reviewer this time and review PAM?

@martinfleis
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@fredshone Thank! Can you please check the references and ensure that the names are rendered? Right now, most of the names are just initials.

@fredshone
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@editorialbot generate pdf

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

@editorialbot
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Five most similar historical JOSS papers:

AgentPy: A package for agent-based modeling in Python
Submitting author: @JoelForamitti
Handling editor: @sbenthall (Active)
Reviewers: @jamesdamillington, @martibosch
Similarity score: 0.8151

LoadProfileGenerator: An Agent-Based Behavior Simulation for Generating Residential Load Profiles
Submitting author: @noah80
Handling editor: @fraukewiese (Active)
Reviewers: @mewilhel, @szkafander
Similarity score: 0.8120

Melodie: Agent-based Modeling in Python
Submitting author: @SongminYu
Handling editor: @jbytecode (Active)
Reviewers: @JoelForamitti, @rusu24edward
Similarity score: 0.8111

High-performance neural population dynamics modeling enabled by scalable computational infrastructure
Submitting author: @a9p
Handling editor: @emdupre (Active)
Reviewers: @richford, @tachukao
Similarity score: 0.8102

Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle
Submitting author: @barneydobson
Handling editor: @crvernon (Active)
Reviewers: @cheginit, @jlarsen-usgs
Similarity score: 0.8099

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

@fredshone
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so sorry @martinfleis ! I saw the weird formatting and thought it was some new concise JOSS style... I am new to .bib.

Anyway looks correct now. Thanks for your patience.

@jofmi
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jofmi commented Oct 9, 2023

Hi @martinfleis, at the moment i have no capacity, sorry!

@SongminYu
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Hi @martinfleis, the work looks very interesting but I have some other pressing tasks at the moment, sorry.

@martinfleis
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Hi @martibosch and @rusu24edward, would you be willing to review this JOSS submission? I believe that it is reasonably close to your expertise. Thanks!

@rusu24edward
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Sorry, I cannot do it

@martibosch
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Hello @martinfleis, thank you for the invitation. Even though the topic interests me, I am afraid that I would rather decline as I am currently swamped. Let me know in some weeks if you still have not found suitable reviewers.

Best,
Martí

@fredshone
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@martinfleis I've gone through the list of reviewers again looking for (more relaxed) relevance, some ideas, but not great ones:

  • There is some application for energy (demand) modelling - eg Gregor Becker
  • There is some application for epidemiology/ABM - eg chrisvoncsefalvay
  • Civil Engineering (most common application of pam is transport modelling which is ~Civil Engineering) - eg dpzhuX
  • General interest in "engineering" - eg msdaldo
  • Data engineering (bit of a stretch as pam is pretty simple) - eg singhpraveen2010

Other than martibosch (🙇🏻 ) there seems a lack of obviously related persons - Is it helpful to propose reviewers from "outside"? I know some likely unbiased third parties.

@martinfleis
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Is it helpful to propose reviewers from "outside"? I know some likely unbiased third parties.

Yes, for sure. Thanks!

@fredshone
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@martinfleis - praneethd7 has volunteered to review!

@martinfleis
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@fredshone it would be better if you could give me just suggestions and let me handle the invitation. For example, I don't see the link between the submission and work of praneethd7 at the moment. Thanks!

@martinfleis
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Hi @jamesdamillington and @dinacmistry, would you be willing to review this JOSS submission? I believe that it is reasonably close to your expertise. Thanks!

@jamesdamillington
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@martinfleis This is a little outside my expertise but looks interesting. I am super busy with teaching, fieldwork and marking before Christmas, but I am more free in January. I suggest you try to find someone with closer expertise, but if you are unable and still need someone in January, please come back to me and I will be able to help then.

@martinfleis
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@jamesdamillington and @martibosch, I am finding it quite tricky to find any suitable reviewers for this. Would you two be willing to accept the invitation under assumption that you'll have more time than usual for that? I think that given the upcoming holiday season, January is perfectly fine timing.

@jamesdamillington
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@martinfleis Yes, that's fine

@martinfleis
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@editorialbot add @jamesdamillington as reviewer

Thanks a lot @jamesdamillington!

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@jamesdamillington added to the reviewers list!

@martibosch
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Hello @martinfleis, sure count me in!

@martinfleis
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@editorialbot add @martibosch as reviewer

Thank you @martibosch!

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@martibosch added to the reviewers list!

@martinfleis
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@editorialbot start review

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OK, I've started the review over in #6097.

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@arfon @jamesdamillington @oliviaguest @martibosch @SongminYu @rusu24edward @fredshone @martinfleis @jofmi @editorialbot