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[REVIEW]: netroles: A Java library for role equivalence analysis in networks #5903
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Review checklist for @abhishektiwariConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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@leifeld - please feel free to create your checklist in this thread. You can do so by following the instructions above. Please let me know if you have any questions. @abhishektiwari - how is the review proceeding? do you have any questions yet? please feel free to post comments here in this thread. You should also feel free to link comments here to open issues in the submission repository. You can open new issues in the submission repository, too. |
@fboehm I will have my initial feedback in by Friday. |
Thank you, @abhishektiwari! If you encounter any difficulties or have questions, please let me know in this thread. Thanks again! |
@muellerj2 Please see my initial feedback. I am still working to verify the functional claims of the software. General checksSubstantial scholarly effort
Project meets borderline well-established software project criteria established by JOSS. Need additional confirmation from author. — Age of software on GitHub is just over 3 months, although it seems software was imported from somewhere else (first commit) @mullerj2 can you confirm how long software has been under active development before publishing to GitHub? DocumentationFunctionality documentationAlthough software is documented to a satisfactory level, for a Java package API documentation is scattered between Software paperQuality of writing
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Review checklist for @leifeldConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Additional commentsWell done, I find the repository to be in very good shape, with the The paper itself feels like it lacks more examples and a conclusion, but I guess that's the desired format at JOSS, and it would only duplicate the I agree with the other reviewer's issue regarding linking the javadoc files in the documentation (likely in the I added one issue regarding a minor documentation glitch but found the documentation to be in good shape otherwise. One question I have is whether @muellerj2 wrote all the code or if the co-author on the Social Networks paper or any of the other The functional programming style is neat. I look forward to seeing more applied research using this package. |
@fboehm Will I need to do anything else? |
@leifeld - Thank you so much for the thorough and helpful review! It would be great if you can review the author's responses to your comments to ensure that the concerns are fully addressed before the submission is published. However, there are no tasks right now that need your immediate attention. |
Thank you, @abhishektiwari for the constructive review! Thanks! |
Regarding substantive scholarly effort: It is the case that this was extracted from another repository. I probably wrote the first pieces of code for role analysis that developed into the core of this library around the end of 2016, when I started working on role equivalences as the topic of my PhD, and have kept developing and extending it since then because I needed it for my academic work, some of which has been published (in 2019 and 2022) and some of which still needs to be. The design of the user API went through some revisions, but had mostly taken its current form in the style of functional programming by early 2020. Originally, I wrote the role equivalence functionality with the intention to make it a module of a larger general-purpose network analysis library, which was supposed to be made open source in the future. However, all other modules are not in a publishable state and their development has been stalled for years. By now, I have to objectively say the original project is essentially abandoned (although I'm not ready yet to give up on it completely). So I extracted the role analysis module from this larger repository to publish it on GitHub, omitting everything which is unusable or not practically relevant to perform role equivalence analysis, and the outcome is this library. |
Thank you for additional context @muellerj2. |
My impression is that papers on R packages in JOSS often contain usage examples. But before I made the paper submission, I checked the published papers on Java libraries and applications in JOSS, and I only found a single paper containing a code example among all of them, and this code example wasn't any longer than the small example in my paper. I guess the issue is that Java needs more boilerplate and is more wordy than a dynamic language like R, so it makes the paper even longer and almost impossible to include a full code example without exceeding the word limit. The paper has already reached the word limit, which means any addition of usage examples would substantially exceed it. So I guess it will have to be @fboehm's call whether some usage examples could be added. If so, I would try to work in some shorter versions of the usage examples in the
I wouldn't say I'm the main author of
The co-author of the Social Networks didn't contribute any code and wasn't involved in the software design of the role analysis code (beyond the ideas and concepts we published on in Social Networks). It also includes none of the code of the Originally, the role analysis core of this library was supposed to become a module of the third iteration of I extracted the role analysis module plus a minimal set of utility classes from the The core of this library -- the role analysis module -- was written by me alone and no one else. But while I have made additions and substantive changes to the utility classes and wrote large portions of the test code and almost all of the documentation for them, many of the utility classes used by the library (specifically containers, network representation and IO) were originally designed and written by someone else. I contacted this person before I published the library on GitHub and asked him as well whether he wanted to appear as a contributor to the library, but he declined. However, if he tells me in the future that he would like his name to appear, I will add it to the repository -- after all, it is his right to decide if and how he is named as a contributor. Still, I wrote most of the code in the repository (at least 80% of the lines of code, likely quite a bit more but I didn't perform an exact count) and all the code for the library's core role analysis functionality. Only the utility classes contain code not written by me, but these classes could be replaced by similar functionality available in other common Java packages (although this would take quite a bit of rewriting effort since the role equivalence analysis code makes widespread use of them). |
@fboehm I'm happy with these explanations and recommend publishing the paper. Thanks for these additional explanations, @muellerj2. As an aside, please don't let visone die. The majority of the ~ 300 publications that use Discourse Network Analyzer benefitted from it. |
@leifeld and @abhishektiwari - Thank you for the thorough and timely reviews! this completes your duties as reviewers of this submission. I hope that we can work together on a future submission. @muellerj2 - the reviewers have recommended your submission for publication. In a moment, I'll create a checklist of items for you and me to complete before final publication. It may take me a few days to complete my tasks. Please feel free to work on the checklist tasks for the author (in the checklist that will appear below in a moment), and please let me know if you have questions. |
Post-Review Checklist for Editor and AuthorsAdditional Author Tasks After Review is Complete
Editor Tasks Prior to Acceptance
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hi, @muellerj2 - I apologize for the long delay before replying. I am now back at work and would like to expedite completion of the publication process. I'll need a day or two to do a few things, including double-checking the updated version of your manuscript. I don't expect it to need many changes, but I want to look over the minor changes you made before I recommend publication. |
@fboehm No problem. The paper was only changed by the following commit compared to the previous version you already checked: muellerj2/netroles@3a32477 This should make it easier for you to decide where to take a closer look in the updated paper. |
@editorialbot generate pdf |
@editorialbot check references |
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@muellerj2 - Thank you - that comment is indeed helpful. The generated pdf looks good. |
@editorialbot recommend-accept |
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👋 @openjournals/csism-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4917, then you can now move forward with accepting the submission by compiling again with the command |
As the track editor, I'll proofread this shortly and get back to you with next steps. |
@muellerj2 - I've suggested some minor changes in muellerj2/netroles#64 - please merge this, or let me know what you disagree with, then we can proceed to acceptance and publication |
@danielskatz I'm fine with these changes and applied them to the paper. |
@editorialbot recommend-accept |
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👋 @openjournals/csism-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4920, then you can now move forward with accepting the submission by compiling again with the command |
@editorialbot accept |
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Congratulations to @muellerj2 (Julian Müller) on your publication!! And thanks to @leifeld and @abhishektiwari for reviewing, and to @fboehm for editing! |
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Thank you @abhishektiwari and @leifeld for reviewing and @fboehm and @danielskatz for handling the paper. |
Submitting author: @muellerj2 (Julian Müller)
Repository: https://github.com/muellerj2/netroles
Branch with paper.md (empty if default branch): paper
Version: v1.0
Editor: @fboehm
Reviewers: @leifeld, @abhishektiwari
Archive: 10.5281/zenodo.10070537
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