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[PRE REVIEW]: extendr: Frictionless bindings for R and Rust #6328
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Five most similar historical JOSS papers: JuliaCall: an R package for seamless integration between R and Julia Bedtoolsr: An R package for genomic data analysis and manipulation rustworkx: A High-Performance Graph Library for Python mlr3: A modern object-oriented machine learning framework in R FEM_2D: A Rust Package for 2D Finite Element Method Computations with Extensive Support for hp-refinement |
@openjournals/dev - for some reason, the |
👋 @CGMossa - thanks for your submission. Can you explain how this is research software, as I'm not sure I see it that way from the paper. What kinds of research papers would you expect to cite this work? |
Thanks for your prompt handling of our submission! This software has broad applicability (as you can see from the diverse affiliations of the authors), but to give you a specific example: the focus of the team at the University of Copenhagen is on research into infectious disease modelling. Specifically, we are using extendR to facilitate implementation of agent-based models of disease spread, where there is a big need for researchers to code up complex models in an efficient language, where most/all of them are based around workflows in R. My own PhD project is on African Swine Fever in domestic pigs and wild boar (and we would cite this paper in future work on specific models), but there are a lot of other similar applications in veterinary epidemiology and human infectious disease modelling. We cited a few of the researchers using Rust for models of ASF in wild boar in the introduction to our paper, but there are many others that are currently using a combination of e.g. C++ and R but would benefit from switching to Rust with an interface in R that we expect to cite extendR. In fact, we see extendR as fulfilling the same remit for R/Rust as Rcpp does for R/C++ - and the relevant article for Rcpp (https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=Rcpp&btnG=) has been cited almost 2000 times! We also mention changeforest https://github.com/mlondschien/changeforest/ which is published research software & paper. They would probably have cited an extendr-reference if it was present at that time. Researchers that mainly write simulation/analysis/visualisation code in R, that occassionally need performance-focused code are one potential target. changeforest is an example of that. In JOSS there is a paper on JuliaCall https://github.com/Non-Contradiction/JuliaCall, https://joss.theoj.org/papers/10.21105/joss.01284 which fulfills the exact same niche we do. However, we cited jlrs, because it brings Rust to Julia (which makes more sense for our paper). I hope that helps to alleviate your concerns but please let me know if you would like further explanation. |
To provide a bit more context extendr plays a core role in this network merge paper that was recently submitted. A key part of the algorithm is written in rust and bindings are provided to R via extendr. Those rust algorithms/routines are then used as a part of a larger algorithm to merge two transit networks. |
Thanks @CGMossa and @JosiahParry - I'm going to ask the JOSS editorial board to consider this issue and your responses, and then we'll make a decision about this, probably in a week or two. |
@editorialbot query scope |
Submission flagged for editorial review. |
@danielskatz thanks for looking at the paper. Could I also add another point to the discussion with the JOSS editorial board: as @CGMossa says, our paper is very similar in scope and purpose to https://joss.theoj.org/papers/10.21105/joss.01284 - which is one of the reasons we sent the extendR paper to JOSS. According to google scholar, the JuliaCall paper has been cited 15 times in a variety of fields, but I actually see the use case for R/Rust integration to be substantially more compelling than that for R/Julia integration - and perhaps eventually (if Rust continues its current growth in popularity) even similar to the use case for R/C++ integration (where the Rcpp article in JSS that @CGMossa mentioned has been very frequently cited). My own JSS article on interfacing R to JAGS (another similar use case to our paper) is by far the most frequently cited of my >100 research publications (https://scholar.google.co.uk/citations?user=Zos2XTkAAAAJ&hl=en), so I am a big believer in the research impact of this kind of software. |
Note: if this passes the scope review, @jbytecode would like to edit it |
@danielskatz That's good - I'm very happy that somebody has already volunteered for editorial duties! I was also contacted by @luciorq who expressed an interest in reviewing the paper, if it passes editorial review. They heard about the paper submission via our discord server but are independent of the extendR project and we have not previously been in contact, so there is no conflict of interest. I couldn't find any other mechanism to suggest reviewers so have done so here - hope that's OK. |
@CGMossa - please see the first comment in this issue, which includes
so basically, yes, we are happy with recommendations for reviewers, but in general don't want them tagged so they don't get notified before an editor chooses to ask them, to not send extra notifications to people... |
@CGMossa - this has passed the scope review, so we'll start the process, by assigning @jbytecode as the editor, and then he'll work on finding reviewers, perhaps with your suggestions. |
@editorialbot assign @jbytecode as editor 🙏 |
Assigned! @jbytecode is now the editor |
@danielskatz - Thank you. I'll be doing my best. Let me take a close look at the submission first. Since I'm familiar with the project, everything will be straightforward. |
@editorialbot check references |
@CGMossa - Hi, thank you for submitting your paper on such a valuable software to JOSS. I am the handling editor. We will be handling whole the stuff during the review process until a final decision is made by our track editor. Upon initial review, I noticed a couple of things that need correction in your BibTeX file (as well as the manuscript), but these can also be addressed after the review as they require only minor changes. We need to identify at least 2 suitable reviewers. It appears you have already suggested one reviewer, and I would be happy to invite them as they seem to have expertise in R. You may also suggest additional reviewers from the potential reviewers' list provided at the top of this issue. I believe including at least one Rustacean who is familiar with the R environment would be beneficial. Please provide the list of potential reviewers without using the '@' character to avoid triggering notifications. Thank you in advance! |
@editorialbot generate pdf |
Five most similar historical JOSS papers: eixport: An R package to export emissions to atmospheric models rustworkx: A High-Performance Graph Library for Python Bedtoolsr: An R package for genomic data analysis and manipulation FEM_2D: A Rust Package for 2D Finite Element Method Computations with Extensive Support for hp-refinement mlr3: A modern object-oriented machine learning framework in R |
@CGMossa - you can also investigate the suggested papers (Five most similar historical JOSS papers) and we can give priority to their authors. |
👋👋👋 Dear @luciorq 👋👋👋 Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)? JOSS publishes articles about open source research software. The submission I'd like you to review is titled: extendr: Frictionless bindings for R and Rust You can find more information at the top of this Github issue (#6328). The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know. This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer. Thank you in advance! |
Thank you very much the guidance on the next steps.
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@CGMossa - Thank you for providing a set of potential reviewers, indeed, that's very helpful. Sure, you can push your commits as we haven't started the review process yet. You can also push your commits of code changes during the review process but this time it wouldn't make breaking changes and/or become a cause of confusing. Changing the content of the manuscript is not usual. |
👋👋👋 Dear @dccsillag and @esteinig 👋👋👋 Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)? JOSS publishes articles about open source research software. The submission I'd like you to review is titled: extendr: Frictionless bindings for R and Rust You can find more information at the top of this Github issue (#6328). The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know. This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer. Thank you in advance! |
@CGMossa - please trigger a |
@editorialbot generate pdf |
Five most similar historical JOSS papers: JuliaCall: an R package for seamless integration between R and Julia eixport: An R package to export emissions to atmospheric models FEM_2D: A Rust Package for 2D Finite Element Method Computations with Extensive Support for hp-refinement mlr3: A modern object-oriented machine learning framework in R Bedtoolsr: An R package for genomic data analysis and manipulation |
👋👋👋 Dear @robmoss 👋👋👋 Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)? JOSS publishes articles about open source research software. The submission I'd like you to review is titled: extendr: Frictionless bindings for R and Rust You can find more information at the top of this Github issue (#6328). The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know. This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer. Thank you in advance! |
@jbytecode in principle I'd be interested in reviewing this paper, but my capacity is extremely limited at the moment — I have impending deadlines for several research contracts — and I don't believe I could complete the review in a timely manner. I have another JOSS review underway, and once I finish it I might be able to review this paper, if you're still searching for reviewers at that point. Sorry! |
Hello! Yes, I'd be happy to review it. |
@editorialbot add @dccsillag as reviewer @dccsillag - thank you for accepting our invitation. whenever we set at least two reviewers, the review will start in a separate thread. I will introduce the review instructions there. thank you. |
@dccsillag added to the reviewers list! |
👋👋👋 Dear @lskatz 👋👋👋 Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)? JOSS publishes articles about open source research software. The submission I'd like you to review is titled: extendr: Frictionless bindings for R and Rust You can find more information at the top of this Github issue (#6328). The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know. This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer. Thank you in advance! |
Dear @jbytecode, Thank you for the invitation to review "extendr: Frictionless bindings for R and Rust" for JOSS. I am intrigued by the subject, given my background in R and bindings to other languages. Looking forward to contributing to the JOSS community. |
@editorialbot add @luciorq as reviewer @luciorq - thank you for accepting our invitation @CGMossa, @dccsillag, @luciorq - I am now starting the review process in a separate thread (issue). The pre-review thread will be automatically closed. See you there. Thank you in advance. |
@luciorq added to the reviewers list! |
@editorialbot start review |
OK, I've started the review over in #6394. |
Hi, thank you for including me. I do not feel like I am enough of an expert in R and Rust to view language bindings between them, but I am comforted that you found enough reviewers to move forward. |
Submitting author: @CGMossa (Mossa Reimert)
Repository: https://github.com/extendr/extendr
Branch with paper.md (empty if default branch): paper
Version: v0.6.0
Editor: @jbytecode
Reviewers: @dccsillag, @luciorq
Managing EiC: Daniel S. Katz
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@CGMossa 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.
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