Closed editorialbot closed 1 month ago
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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
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
Paper file info:
📄 Wordcount for paper.md
is 989
✅ The paper includes a Statement of need
section
License info:
🟡 License found: GNU General Public License v3.0
(Check here for OSI approval)
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Five most similar historical JOSS papers:
nsink: An R package for flow path nitrogen removal estimation
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Similarity score: 0.6986
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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.
👋 @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!
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Invitation to edit this submission sent!
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 - 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.
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Assigned! @Nikoleta-v3 is now the editor
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?
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?
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.
👋🏻 @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!
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...
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?
I will have to consult the project team on this one.
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.
@Nikoleta-v3 I'm happy to help, but I do want to mention that I'm not an R expert.
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.
@PieterjanRobbe Amazing, thank you! That is fine; between myself and the second reviewer, it should be fine!
@editorialbot add @PieterjanRobbe as reviewer
@PieterjanRobbe added to the reviewers list!
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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.
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
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.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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.
@wcjochem amazing thank you! 🙏🏻
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@wcjochem added to the reviewers list!
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OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7047.
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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