[REVIEW]: DataRepExp: a R shiny Application that makes Data FAIR for Data Repositories
editorialbot opened this issue · comments
Submitting author: @RoryChenXY (Xinyue (Rory) Chen)
Repository: https://github.com/RoryChenXY/DataRepExp_public
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @crvernon
Reviewers: @elimillera, @pydemull, @ZekeMarshall
Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/08ca6a54216bb27b7ec37ead6bf951cb"><img src="https://joss.theoj.org/papers/08ca6a54216bb27b7ec37ead6bf951cb/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/08ca6a54216bb27b7ec37ead6bf951cb)
Reviewers and authors:
Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@elimillera & @pydemull & @ZekeMarshall, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:
@editorialbot generate my checklist
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @crvernon know.
✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨
Checklists
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Software report:
github.com/AlDanial/cloc v 1.90 T=0.03 s (1592.2 files/s, 284529.5 lines/s)
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Language files blank comment code
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R 28 792 584 5098
CSV 7 0 0 550
TeX 1 39 0 322
Markdown 5 103 0 248
CSS 2 14 0 90
YAML 1 1 4 18
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SUM: 44 949 588 6326
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Commit count by author:
30 Rory
13 RoryXChen
Paper file info:
📄 Wordcount for paper.md is 1190
✅ The paper includes a Statement of need section
License info:
✅ License found: MIT License (Valid open source OSI approved license)
👋 @RoryChenXY, @elimillera, @pydemull, and @ZekeMarshall - This is the review thread for the paper. All of our communications will happen here from now on.
Please read the "Reviewer instructions & questions" in the first comment above.
Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.
The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #6693 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.
We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/sdata.2016.18 is OK
- 10.1371/journal.pcbi.1006038 is OK
- 10.1371/journal.pcbi.1009768 is OK
- 10.1007/s10654-023-00997-3 is OK
- 10.1007/s10654-022-00916-y is OK
- 10.1007/s10654-020-00633-4 is OK
- 10.1007/978-3-319-24277-4 is OK
- 10.18637/jss.v040.i03 is OK
- 10.1201/9780429447273 is OK
- 10.21105/joss.01686 is OK
- 10.1007/978-3-319-24277-4 is OK
- 10.18637/jss.v040.i03 is OK
- 10.1201/9780429447273 is OK
- 10.21105/joss.01686 is OK
MISSING DOIs
- No DOI given, and none found for title: Dementias Platform Australia
- No DOI given, and none found for title: Alzheimer’s Disease Data Initiative
- No DOI given, and none found for title: Dementias Platform Australia Data Portal
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: dplyr: A Grammar of Data Manipulation
- No DOI given, and none found for title: DT: A Wrapper of the JavaScript Library DataTables
- No DOI given, and none found for title: fontawesome: Easily Work with Font Awesome Icons
- No DOI given, and none found for title: forcats: Tools for Working with Categorical Variab...
- No DOI given, and none found for title: htmltools: Tools for HTML
- No DOI given, and none found for title: magrittr: A Forward-Pipe Operator for R
- No DOI given, and none found for title: purrr: Functional Programming Tools
- No DOI given, and none found for title: readr: Read Rectangular Text Data
- No DOI given, and none found for title: scales: Scale Functions for Visualization
- No DOI given, and none found for title: shiny: Web Application Framework for R
- No DOI given, and none found for title: shinydashboard: Create Dashboards with Shiny
- No DOI given, and none found for title: shinyjs: Easily Improve the User Experience of You...
- No DOI given, and none found for title: shinyWidgets: Custom Inputs Widgets for Shiny
- No DOI given, and none found for title: stringr: Simple, Consistent Wrappers for Common St...
- No DOI given, and none found for title: tibble: Simple Data Frames
- No DOI given, and none found for title: tidyr: Tidy Messy Data
- No DOI given, and none found for title: useful: A Collection of Handy, Useful Functions
INVALID DOIs
- None
Review checklist for @ZekeMarshall
Conflict of interest
- I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.
Code of Conduct
- I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- Repository: Is the source code for this software available at the https://github.com/RoryChenXY/DataRepExp_public?
- License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- Contribution and authorship: Has the submitting author (@RoryChenXY) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
- Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.
Functionality
- Installation: Does installation proceed as outlined in the documentation?
- Functionality: Have the functional claims of the software been confirmed?
- Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
Documentation
- A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
Software paper
- Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
- State of the field: Do the authors describe how this software compares to other commonly-used packages?
- Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
Hi @RoryChenXY, I'm just working through my review checklist now. Have you considered making versioned releases of DataRepExp_public? One other question, is there a "DataRepExp_private" repository? If so do you plan to keep future developments synchronised between these repositories?
Hi @RoryChenXY, I'm just working through my review checklist now. Have you considered making versioned releases of DataRepExp_public? One other question, is there a "DataRepExp_private" repository? If so do you plan to keep future developments synchronised between these repositories?
Hi @ZekeMarshall. 1. I think making versioned releases would be great; 2. There is a private repository that uses some AWS services and links to the sensitive data we use, with domain-specific variables. In the future, if we add more modules/functions in the private repository, I will update the public one manually. Due to security reasons, no synchronisation would happen between repositories.
Thanks,
Rory
Hi @RoryChenXY, I'm just working through my review checklist now. Have you considered making versioned releases of DataRepExp_public? One other question, is there a "DataRepExp_private" repository? If so do you plan to keep future developments synchronised between these repositories?
Hi @ZekeMarshall. 1. I think making versioned releases would be great; 2. There is a private repository that uses some AWS services and links to the sensitive data we use, with domain-specific variables. In the future, if we add more modules/functions in the private repository, I will update the public one manually. Due to security reasons, no synchronisation would happen between repositories.
Thanks, Rory
Hi @RoryChenXY ,
That sounds good! Before I tick off the "Reproducibility" checklist item I would prefer that there was an initial versioned release.
Cheers,
Zeke
Hi @RoryChenXY , I don't think I can tick the "Automated tests" checklist item, as there are no tests in the repository. I think that all functions in the repository should be tested, which in DataRepExp consist of the functions in the vis_functions.R file. You could also test your modules, though I don't think that's strictly necessary. Best regards, Zeke
Hi @RoryChenXY , to tick of the "Installation" and "Reproducibility" checklist items I think the repository requires dependencies to be recorded, i'd use {renv} to do this. Best regards, Zeke
Review checklist for @pydemull
Conflict of interest
- I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.
Code of Conduct
- I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- Repository: Is the source code for this software available at the https://github.com/RoryChenXY/DataRepExp_public?
- License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- Contribution and authorship: Has the submitting author (@RoryChenXY) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
- Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.
Functionality
- Installation: Does installation proceed as outlined in the documentation?
- Functionality: Have the functional claims of the software been confirmed?
- Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
Documentation
- A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
Software paper
- Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
- State of the field: Do the authors describe how this software compares to other commonly-used packages?
- Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
Hi @RoryChenXY , regarding co-authorship, while JOSS does not require mentioning the kinds of the contributions from the different co-authors, I think it could be good to mention somewhere (eg, in the footer of the app or on a dedicated page of the app, or in the repo) what have been these kinds of contributions (eg, XX, YY and ZZ, ..., conceived the app (design, aim, features, etc), and XX and YY developed the app (the code)). A potential interest could be to provide some clues about the confidence a user can have in the app (especially if it is a new piece of software that has not been fully scrutinized by the community) : the more there are people who have the skills to check the code, the less there are risks of undetected bugs (I think). I am not saying that a single person is not able to provide perfectly correct code of course. It is not mandatory so I check the box for this item.
👋 @RoryChenXY, @elimillera, @pydemull, and @ZekeMarshall
Just checking in to see how things are going with this review! Could you provide a short update here in this thread? Thanks!
👋 @RoryChenXY, @elimillera, @pydemull, and @ZekeMarshall
Just checking in to see how things are going with this review! Could you provide a short update here in this thread? Thanks!
Hi @crvernon , all good, just waiting for @RoryChenXY to reply to my queries above. Once resolved i'll then proceed with the other checklist items!
Review checklist for @elimillera
Conflict of interest
- I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.
Code of Conduct
- I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- Repository: Is the source code for this software available at the https://github.com/RoryChenXY/DataRepExp_public?
- License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- Contribution and authorship: Has the submitting author (@RoryChenXY) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
- Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.
Functionality
- Installation: Does installation proceed as outlined in the documentation?
- Functionality: Have the functional claims of the software been confirmed?
- Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
Documentation
- A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
Software paper
- Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
- State of the field: Do the authors describe how this software compares to other commonly-used packages?
- Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
👋 @RoryChenXY, @elimillera, @pydemull, and @ZekeMarshall
Just checking in to see how things are going with this review! Could you provide a short update here in this thread? Thanks!
Working through this in the next few days. Thanks!
e going with this review! Could you provide a short update here i
Apologies - I was on sick leave, getting on it now
No problem @RoryChenXY! Thanks!
Dear All,
For better reproducibility, I have been experimenting with 'testthat' and unit testing, and realised my work needs to be improved so it can be used by others. This is the first time I am sharing my code with others.
I think the best way is to organise the app as a package.
I am reading https://r-pkgs.org/ and https://engineering-shiny.org/ at the moment.
Apologise for the delays, but there is a learning curve. I will do my best.
Please let me know if you don't think the package is necessary.
Thanks,
Rory
👋 @RoryChenXY - first, I am so happy that you are sharing your code for the first time! Our goal here at JOSS is to make sure we help you put together the best product possible.
As far as the tests go, I am glad you are working on these. They will make your code more reliable and stable.
Your reviewers @elimillera, @pydemull, and @ZekeMarshall can provide some solid feedback and help as you go through this process. Don't hesitate to reach out! Thanks!
Hi @RoryChenXY, just to say you that the two books you have mentioned are the books I have used to build my first Shiny app as a package. Both books will by very useful. The {golem} package (in relation with this book: https://engineering-shiny.org/) allows a fast implementation of the general structure of your repository so that it can be used as a package. The book by Hadley Wickham provides very useful tips for general and common tasks. Personally, I have used the package {shinytest2} to test if the app works correctly. Testing also the basic functions of the app outside the app (which should be done) is not the hardder part. Testing if the app correctly works (correct inputs, correct outputs, etc.) is unfortunately more complicated, but this will render the whole app of a higher quality. I am not a software engineer (not at all) but I will be happy to help if I can.
@crvernon My check is complete. I have opened the following issues:
As noted by the other editors, some tests would also be good to add for the application, generally I've seen this done in package framework, however that isn't a requirement and just a testthat directory should work without the package framework.
Nice work @RoryChenXY! Let me know if you would like me to expand on any of the points above.
👋 @RoryChenXY - it looks like you have some good feedback from @elimillera and @pydemull. Please report here as you have any questions for feedback to the reviewers. Thanks!