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[PRE REVIEW]: 4DModeller: a spatio-temporal modelling package #6996

Closed editorialbot closed 1 month ago

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@rwestaway<!--end-author-handle-- (Richard Westaway) Repository: https://github.com/4DModeller/fdmr Branch with paper.md (empty if default branch): JOSS Version: v0.2.0 Editor: !--editor-->@Nikoleta-v3<!--end-editor-- Reviewers: @PieterjanRobbe, @wcjochem Managing EiC: Daniel S. Katz

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Markdown: [![status](https://joss.theoj.org/papers/0f2a730dc4786def16ae43c849e07a73/status.svg)](https://joss.theoj.org/papers/0f2a730dc4786def16ae43c849e07a73)

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editorialbot commented 1 month ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot commented 1 month ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1785/0220170246 is OK
- 10.1111/2041-210X.13168 is OK
- 10.3030/694188 is OK
- 10.1111/j.1467-9868.2008.00700.x is OK
- 10.2307/j.ctvjf9vz4 is OK
- 10.21105/joss.03914 is OK
- 10.25436/E27C7F is OK
- 10.1038/s41598-024-60964-0 is OK
- 10.1214/17-AOAS1078 is OK
- 10.1093/gji/ggac365 is OK

MISSING DOIs

- No DOI given, and none found for title: inlabru

INVALID DOIs

- None
editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (746.5 files/s, 499974.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              4              0              0          28871
Rmd                             17           1024           1364           1959
R                               21            289            532           1848
TeX                              2            110              0           1077
XML                              1              0             12            691
Markdown                         8            185              0            645
YAML                             4             11             12            210
JSON                             1              0              0              8
-------------------------------------------------------------------------------
SUM:                            58           1619           1920          35309
-------------------------------------------------------------------------------

Commit count by author:

   407  Gareth Jones
    41  Anrijs K. Abele
    40  XueqingYin
    18  mnky9800n
    12  John Aiken
     7  desireetreichler
     5  Anrijs Abele
     4  Tian Li
     3  Désirée Treichler
     2  Kristoffer Aalstad
     1  Alexander Minakov
     1  El
     1  Jonathan Bamber
     1  Julie Røste
     1  mmazzolini
editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 989

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

nsink: An R package for flow path nitrogen removal estimation Submitting author: @jhollist Handling editor: @crvernon (Active) Reviewers: @jmp75, @ldecicco-USGS, @jmp75 Similarity score: 0.6986

GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields Submitting author: @PieterjanRobbe Handling editor: @jbytecode (Active) Reviewers: @ziyiyin97, @shahmoradi Similarity score: 0.6979

WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models Submitting author: @aurorarossi Handling editor: @fraukewiese (Active) Reviewers: @ranocha, @StanczakDominik, @miguelraz Similarity score: 0.6978

parafields: A generator for distributed, stationary Gaussian processes Submitting author: @dokempf Handling editor: @diehlpk (Active) Reviewers: @shahmoradi, @gchure Similarity score: 0.6949

dlmmc: Dynamical linear model regression for atmospheric time-series analysis Submitting author: @justinalsing Handling editor: @danielskatz (Active) Reviewers: @Chilipp, @taqtiqa-mark Similarity score: 0.6946

⚠️ 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 considering asking the reviewers of these papers to review again for JOSS.

danielskatz commented 1 month ago

👋 @Nikoleta-v3 - Here's a second submission that I wonder if you could edit? If you can take this one or the other, it would be great!

danielskatz commented 1 month ago

@editorialbot invite @Nikoleta-v3

editorialbot commented 1 month ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

danielskatz commented 1 month ago

@editorialbot invite @Nikoleta-v3 as editor

editorialbot commented 1 month ago

Invitation to edit this submission sent!

rwestaway commented 1 month ago

Potential reviewers based on topic areas (none are known to us): Fernando de Pol Mayer, James Mba Azam, Nicholas Tierney, wcjochem, adithirgis, thomaspinder, stevenpawley

Nikoleta-v3 commented 1 month ago

👋 @Nikoleta-v3 - Here's a second submission that I wonder if you could edit? If you can take this one or the other, it would be great!

@danielskatz 👋🏻 I'm happy to review this submission 😄 Unfortunately, I can't do both at the moment.

Nikoleta-v3 commented 1 month ago

@editorialbot me as editor

editorialbot commented 1 month ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Nikoleta-v3 commented 1 month ago

@editorialbot commands

editorialbot commented 1 month ago

Hello @Nikoleta-v3, here are the things you can ask me to do:


# List all available commands
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Nikoleta-v3 commented 1 month ago

@editorialbot assign me as editor

editorialbot commented 1 month ago

Assigned! @Nikoleta-v3 is now the editor

Nikoleta-v3 commented 1 month ago

Thank you for your submission and for suggesting reviewers @rwestaway. I have successfully managed to install the package and run a few examples. The package is very well documented, and the readme is very clear and well organized 😄

I am going to contact some of the authors of recent publications as well (see https://github.com/openjournals/joss-reviews/issues/6996#issuecomment-2230669081) to see if they can review the paper. In the meantime, could you please address some of my comments and questions?

Paper

There are some minor typos in the paper:

Also in the paper, you have two references for inlabru. Their Methods in Ecology and Evolution paper and the GitHub repository. Is there a reason for that?

Tests

I see that you have some tests. Could you include some information on how to run the test suite? I really like your contribution guidelines; they are short and to the point. Maybe adding the test information there? or would be a bit much?

Whatever you decide, it would just be useful to know how to run the tests locally since the tests run when people open pull requests.

Nikoleta-v3 commented 1 month ago

👋🏻 @jhollist @PieterjanRobbe @wcjochem @thomaspinder would any of you be willing to review this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission I'd like you to review is titled: "4DModeller: a spatio-temporal modelling package". You can find more information at the top of this Github issue 🆙

Please let me know if you're available 😄 Thank you!

rwestaway commented 1 month ago

Thank you for your submission and for suggesting reviewers @rwestaway. I have successfully managed to install the package and run a few examples. The package is very well documented, and the readme is very clear and well organized 😄

I am going to contact some of the authors of recent publications as well (see #6996 (comment)) to see if they can review the paper. In the meantime, could you please address some of my comments and questions?

Paper

There are some minor typos in the paper:

  • Line 27: "behaves"
  • Line 35: "postcode"
  • Line 72: "by the UK."

Also in the paper, you have two references for inlabru. Their Methods in Ecology and Evolution paper and the GitHub repository. Is there a reason for that?

Tests

I see that you have some tests. Could you include some information on how to run the test suite? I really like your contribution guidelines; they are short and to the point. Maybe adding the test information there? or would be a bit much?

Whatever you decide, it would just be useful to know how to run the tests locally since the tests run when people open pull requests.

Thank you @Nikoleta-v3 for your prompt feedback. Should we make changes to the paper.md file as we go along or is that now 'frozen' until all reviewers have responded? We haven't submitted to JOSS before so are unsure of the process...

Paper

Typos will be corrected.

The distinction is between (1) the applications/tutorials of inlabru which are only available via the GitHub repository (cited as Lindgren et al., 2024) and (2) the underlying statistics/method for which the package authors provide two references at https://inlabru-org.github.io/inlabru/authors.html#citation (Bachl et al., 2019 and Yuan et al., 2017). Does that make sense or does it need further clarification in the text?

Tests

I will have to consult the project team on this one.

mnky9800n commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (746.5 files/s, 499974.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              4              0              0          28871
Rmd                             17           1024           1364           1959
R                               21            289            532           1848
TeX                              2            110              0           1077
XML                              1              0             12            691
Markdown                         8            185              0            645
YAML                             4             11             12            210
JSON                             1              0              0              8
-------------------------------------------------------------------------------
SUM:                            58           1619           1920          35309
-------------------------------------------------------------------------------

Commit count by author:

   407    Gareth Jones
    41    Anrijs K. Abele
    40    XueqingYin
    18    mnky9800n
    12    John Aiken
     7    desireetreichler
     5    Anrijs Abele
     4    Tian Li
     3    Désirée Treichler
     2    Kristoffer Aalstad
     1    Alexander Minakov
     1    El
     1    Jonathan Bamber
     1    Julie Røste
     1    mmazzolini

FYI @mnky9800n is John Aiken and that is me. so don't know why it counts me separate but it s not a big deal i guess.

PieterjanRobbe commented 1 month ago

@Nikoleta-v3 I'm happy to help, but I do want to mention that I'm not an R expert.

Nikoleta-v3 commented 1 month ago

Thank you @Nikoleta-v3 for your prompt feedback. Should we make changes to the paper.md file as we go along or is that now 'frozen' until all reviewers have responded? We haven't submitted to JOSS before so are unsure of the process...

Either is fine! If you push to the JOSS branch, everything will be updated. To be honest, I used to wait until I found reviewers to give any feedback on the paper, but since finding reviewers can be quite challenging at times, I started giving feedback beforehand so there is not too much time wasted. This is new territory for me too, haha.

I think you are fine to make the changes, at least the paper changes, and push so the reviewers will have the latest version with the corrections.

Paper

Typos will be corrected.

The distinction is between (1) the applications/tutorials of inlabru which are only available via the GitHub repository (cited as Lindgren et al., 2024) and (2) the underlying statistics/method for which the package authors provide two references at https://inlabru-org.github.io/inlabru/authors.html#citation (Bachl et al., 2019 and Yuan et al., 2017). Does that make sense or does it need further clarification in the text?

Thank you, I understand; I believe it's fine as it is!

Tests

I will have to consult the project team on this one.

Great; thank you.

Nikoleta-v3 commented 1 month ago

@PieterjanRobbe Amazing, thank you! That is fine; between myself and the second reviewer, it should be fine!

Nikoleta-v3 commented 1 month ago

@editorialbot add @PieterjanRobbe as reviewer

editorialbot commented 1 month ago

@PieterjanRobbe added to the reviewers list!

rwestaway commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields Submitting author: @PieterjanRobbe Handling editor: @jbytecode (Active) Reviewers: @ziyiyin97, @shahmoradi Similarity score: 0.7018

WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models Submitting author: @aurorarossi Handling editor: @fraukewiese (Active) Reviewers: @ranocha, @StanczakDominik, @miguelraz Similarity score: 0.6996

nsink: An R package for flow path nitrogen removal estimation Submitting author: @jhollist Handling editor: @crvernon (Active) Reviewers: @jmp75, @ldecicco-USGS, @jmp75 Similarity score: 0.6990

dlmmc: Dynamical linear model regression for atmospheric time-series analysis Submitting author: @justinalsing Handling editor: @danielskatz (Active) Reviewers: @Chilipp, @taqtiqa-mark Similarity score: 0.6969

parafields: A generator for distributed, stationary Gaussian processes Submitting author: @dokempf Handling editor: @diehlpk (Active) Reviewers: @shahmoradi, @gchure Similarity score: 0.6962

⚠️ 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 considering asking the reviewers of these papers to review again for JOSS.

wcjochem commented 1 month ago

Please let me know if you're available 😄 Thank you! @Nikoleta-v3 I'm happy to help with this, if you still need another reviewer

rwestaway commented 1 month ago

Tests

I will have to consult the project team on this one.

Great; thank you.

@Nikoleta-v3 - To respond to your query, the testing suite is a relic of some old code so thank you for flagging that! At the time we had some ideas for testing meshes, and other topics, but as it stands we haven't really built it out or developed it further. However it is something planned for future work.

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields Submitting author: @PieterjanRobbe Handling editor: @jbytecode (Active) Reviewers: @ziyiyin97, @shahmoradi Similarity score: 0.7019

WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models Submitting author: @aurorarossi Handling editor: @fraukewiese (Active) Reviewers: @ranocha, @StanczakDominik, @miguelraz Similarity score: 0.6996

nsink: An R package for flow path nitrogen removal estimation Submitting author: @jhollist Handling editor: @crvernon (Active) Reviewers: @jmp75, @ldecicco-USGS, @jmp75 Similarity score: 0.6988

dlmmc: Dynamical linear model regression for atmospheric time-series analysis Submitting author: @justinalsing Handling editor: @danielskatz (Active) Reviewers: @Chilipp, @taqtiqa-mark Similarity score: 0.6968

parafields: A generator for distributed, stationary Gaussian processes Submitting author: @dokempf Handling editor: @diehlpk (Active) Reviewers: @shahmoradi, @gchure Similarity score: 0.6962

⚠️ 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 considering asking the reviewers of these papers to review again for JOSS.

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields Submitting author: @PieterjanRobbe Handling editor: @jbytecode (Active) Reviewers: @ziyiyin97, @shahmoradi Similarity score: 0.7021

WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models Submitting author: @aurorarossi Handling editor: @fraukewiese (Active) Reviewers: @ranocha, @StanczakDominik, @miguelraz Similarity score: 0.6999

nsink: An R package for flow path nitrogen removal estimation Submitting author: @jhollist Handling editor: @crvernon (Active) Reviewers: @jmp75, @ldecicco-USGS, @jmp75 Similarity score: 0.6989

dlmmc: Dynamical linear model regression for atmospheric time-series analysis Submitting author: @justinalsing Handling editor: @danielskatz (Active) Reviewers: @Chilipp, @taqtiqa-mark Similarity score: 0.6970

parafields: A generator for distributed, stationary Gaussian processes Submitting author: @dokempf Handling editor: @diehlpk (Active) Reviewers: @shahmoradi, @gchure Similarity score: 0.6964

⚠️ 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 considering asking the reviewers of these papers to review again for JOSS.

Nikoleta-v3 commented 1 month ago

@wcjochem amazing thank you! 🙏🏻

Nikoleta-v3 commented 1 month ago

@editorialbot add @wcjochem as reviewer

editorialbot commented 1 month ago

@wcjochem added to the reviewers list!

Nikoleta-v3 commented 1 month ago

@editorialbot start review

editorialbot commented 1 month ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7047.