Closed editorialbot closed 2 months ago
editorialbot
commented
3 months ago 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 commandsFor example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdfReference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.jchromb.2019.04.009 is OK
- 10.1021/acs.analchem.1c02220 is OK
- 10.1021/acs.analchem.9b02983 is OK
- 10.32614/RJ-2022-050 is OK
- 10.1186/s12859-023-05533-4 is OK
- 10.1021/ac800692c is OK
- 10.3390/metabo12020137 is OK
- 10.1201/9780429447273 is OK
- 10.1021/ac051437y is OK
MISSING DOIs
- No DOI given, and none found for title: Shiny: Web Application Framework for R
- No DOI given, and none found for title: Squallms: Speedy Quality Assurance via Lasso Label...
INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.90 T=0.01 s (1108.6 files/s, 166910.2 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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R 9 105 489 835
YAML 2 49 78 237
TeX 1 10 0 147
Rmd 1 80 113 135
Markdown 3 41 0 90
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SUM: 16 285 680 1444
-------------------------------------------------------------------------------Commit count by author:
131 wkumler
2 William Kumler
1 WilliamPaper file info:
📄 Wordcount for paper.md is 1013
✅ The paper includes a Statement of need section
editorialbot
commented
3 months ago License info:
🟡 License found: Other (Check here for OSI approval)
editorialbot
commented
3 months ago :point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
editorialbot
commented
3 months ago Five most similar historical JOSS papers:
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⚠️ 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.
wkumler
commented
3 months ago Listing a few potential reviewers from the list and some thoughts about their relevant expertise:
Kevin-Mattheus-Moerman
commented
2 months ago @wkumler thanks for this submission. As AEiC I'm here to help with initial steps. Note that last week I assigned the query-scope label. This triggers a scope review by the editorial board. I've done this because of the relatively small size of the project. The scope review will determine if this work conforms to our substantial scholarly effort criteria, and will take about 2 weeks to complete.
Kevin-Mattheus-Moerman
commented
2 months ago @wkumler the editorial board has concluded the scope review for this submission. Unfortunately it is not deemed in scope as it stands. Besides the fact that the code base is rather small and the functionality relatively narrow, there were also concerns raised in terms of "maturity". It was recommended that the authors first push for acceptance in Bioconductor. This will likely require various improvements, such as a reduction of the number of dependencies, and also reduction in the use of global variables. We'd welcome a potential re-submission at such a later point, especially when accompanied by a potential expansion of the functionality.
We will now proceed to reject this submission. Note however, this rejection does not mean the work is not useful or not well put together, in simply means that for the above reasons it is not in scope for JOSS as it stands.
Kevin-Mattheus-Moerman
commented
2 months ago @editorialbot reject
editorialbot
commented
2 months ago Paper rejected.
wkumler
commented
2 months ago @Kevin-Mattheus-Moerman Thank you for the feedback, and thank you as well to the editorial board for considering the submission! I am interested in resubmitting at a future point and so could use some additional comments about what else JOSS is looking for in terms of maturity.
squallms is actually already on Bioconductor (https://bioconductor.org/packages/devel/bioc/html/squallms.html), admittedly only in the devel branch because I missed the code freeze cutoff for 3.19squallms has ~15 direct dependencies, many of which are likely to be already installed on user's systems (e.g. the tidyverse, shiny, plotly, graphics, etc.). This doesn't feel like a crazy amount, and removing any of these would reduce the functionality of the package as a whole or require code duplication. Is it possible that JOSS is concerned about the number of recursive dependencies? xcms, for example, has over one hundred packages that it requires but I'm not sure what to do about that if I'd still like to be part of the Bioconductor ecosystem.globalVariables function is used to avoid warnings thrown during package build with non-standard evaluation (e.g. that required by data.table and dplyr).My current plan with this project is to wait to resubmit to JOSS until Bioconductor 3.20 releases (in October) with squallms included, during which I'll work on resolving some of the feature-requests I've got on the Github page. My colleagues and I are already using the package (and have seen interest from other institutions despite the relatively narrow scope) and the goal behind submitting it to JOSS was to avoid having to document the functions encapsulated here in the Methods sections, so perhaps I'll identify additional areas for improvement as we continue to use it. I can also expand the documentation and vignette selection to better emphasize how squallms interfaces with existing MS software such as Skyline, MSDIAL, and MzMine. Would it be better suited for JOSS if that's done?
Submitting author: !--author-handle-->@wkumler<!--end-author-handle-- (William Kumler) Repository: https://github.com/wkumler/squallms Branch with paper.md (empty if default branch): manuscript Version: 0.99.6 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman
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