[PRE REVIEW]: squallms: Squashing qualms with speedy quality assurance via lasso labeling for untargeted mass spectrometry data

[editorialbot]

Submitting author: @wkumler (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

Status

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Reference 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

[editorialbot]

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
-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------
SUM:                            16            285            680           1444
-------------------------------------------------------------------------------

Commit count by author:

   131	wkumler
     2	William Kumler
     1	William

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1013

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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[wkumler]

Listing a few potential reviewers from the list and some thoughts about their relevant expertise:

1. hechth: Previous experience reviewing metabolomics R packages in JOSS (patRoon)
2. adafefe: Chromatography and metabolomics experience plus R
3. joewandy: Metabolomics and R experience
4. luciorq: Broader expertise with Shiny apps and R packages in bioinformatics
5. salix-d: Broader expertise with Shiny apps and R packages in bioinformatics

[Kevin-Mattheus-Moerman]

@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]

@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]

@editorialbot reject

[editorialbot]

Paper rejected.

[wkumler]

@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 3.19
• Reducing the number of dependencies is an admirable goal and one that I did take seriously when writing the package, so I'm interested in additional advice about how many is too many. squallms 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.
• I'm not sure at all what a reduction in global variables would look like - I don't currently assign anything to the global environment (as is required by Bioconductor) and the 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?