[REVIEW]: dtrackr: An R package for tracking the provenance of data #4707

editorialbot · 2022-08-24T17:05:37Z

Submitting author: @robchallen (Robert Challen)
Repository: https://github.com/terminological/dtrackr
Branch with paper.md (empty if default branch): main
Version: 0.2.5-joss
Editor: @ajstewartlang
Reviewers: @debruine, @craig-willis
Archive: 10.5281/zenodo.7433514

Status

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Markdown: [![status](https://joss.theoj.org/papers/47d093cc95dae17d546046bc5ac87475/status.svg)](https://joss.theoj.org/papers/47d093cc95dae17d546046bc5ac87475)

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Reviewer instructions & questions

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Checklists

📝 Checklist for @craig-willis

📝 Checklist for @debruine

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-08-24T17:05:38Z

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editorialbot · 2022-08-24T17:05:40Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.15 s (974.5 files/s, 210098.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           104           5131           1342          18366
R                               13            348           1014           1416
SVG                              2              0              1            956
JavaScript                       6            109             62            442
CSS                              4             99             49            431
Rmd                              5            209            259            333
TeX                              2             34              0            240
Markdown                         5             79              0            237
YAML                             4             17             10             78
-------------------------------------------------------------------------------
SUM:                           145           6026           2737          22499
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-08-24T17:05:41Z

Wordcount for paper.md is 841

editorialbot · 2022-08-24T17:05:53Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1136/bmj.c332 is OK
- 10.1186/s12916-014-0241-z is OK
- 10.1371/journal.pmed.1001885 is OK
- 10.1371/journal.pmed.1001711 is OK
- 10.5121/IJDMS.2011.3207 is OK
- 10.1371/journal.pmed.0040297 is OK
- 10.7326/M18-1376 is OK
- 10.21105/joss.01686 is OK
- 10.1136/bmj.n579 is OK
- 10.2139/ssrn.4087373 is OK
- 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-08-24T17:07:13Z

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

craig-willis · 2022-08-24T18:11:17Z

Review checklist for @craig-willis

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/terminological/dtrackr?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@robchallen) 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

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?

robchallen · 2022-08-25T09:39:24Z

I just wanted to mention that in the branch here under review, the README.md instructions say that "dtrackr" is not yet on CRAN.

This is not correct and the version in the joss review branch (release-0.2.4) of dtrackr is now on CRAN and can be installed with a install.packages("dtrackr") command.

I'm holding back on updating the documentation until I get comments back from you guys. Then I'll make any outstanding fixes update the documentation and push a 0.2.5 release through the CRAN submission process (with the updated installation instructions showing it is on CRAN).

I've just made the exact same mistake on another package I'm submitting to CRAN :-)

ajstewartlang · 2022-10-03T15:20:36Z

👋 @debruine how's your review going?

robchallen · 2022-10-04T23:46:53Z

I've been working through @craig-willis comments, and made quite a few updates. These are in a new branch joss-fixes-0.2.4.9000. Would it be better to do additional review there?

debruine · 2022-10-05T07:06:34Z

I’m sorry I got swamped with work and am running late. I’ll start my review in this branch and aim to complete by Monday.

…

On 5 Oct 2022, at 00:47, Rob Challen ***@***.***> wrote: I've been working through @craig-willis comments, and made quite a few updates. These are in a new branch joss-fixes-0.2.4.9000. Would it be better to do additional review there? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

ajstewartlang · 2022-10-05T07:39:13Z

I've been working through @craig-willis comments, and made quite a few updates. These are in a new branch joss-fixes-0.2.4.9000. Would it be better to do additional review there?

Sure - I'll set that as the review branch now.

ajstewartlang · 2022-10-05T07:39:21Z

@editorialbot set joss-fixes-0.2.4.9000 as branch

editorialbot · 2022-10-05T07:39:24Z

Done! branch is now joss-fixes-0.2.4.9000

craig-willis · 2022-10-07T18:02:58Z

@editorialbot generate pdf

editorialbot · 2022-10-07T18:05:00Z

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

debruine · 2022-10-11T10:09:30Z

Review checklist for @debruine

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/terminological/dtrackr?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@robchallen) 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?

robchallen · 2022-12-13T18:38:58Z

@Kevin-Mattheus-Moerman thank you. fixed that.

Kevin-Mattheus-Moerman · 2022-12-13T20:36:06Z

@editorialbot recommend-accept

editorialbot · 2022-12-13T20:36:07Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-12-13T20:37:36Z

👋 @openjournals/bcm-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#3802, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot · 2022-12-13T20:37:47Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1136/bmj.c332 is OK
- 10.1186/s12916-014-0241-z is OK
- 10.1371/journal.pmed.1001885 is OK
- 10.1371/journal.pmed.1001711 is OK
- 10.5121/IJDMS.2011.3207 is OK
- 10.1371/journal.pmed.0040297 is OK
- 10.7326/M18-1376 is OK
- 10.21105/joss.01686 is OK
- 10.1136/bmj.n579 is OK
- 10.2139/ssrn.4087373 is OK
- 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N is OK
- 10.2218/ijdc.v16i1.763 is OK
- 10.1101/2022.06.29.22277044 is OK
- 10.21105/joss.02959 is OK
- 10.1145/3311955 is OK
- 10.3390/informatics5010012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2022-12-13T22:13:30Z

@editorialbot set main as branch

editorialbot · 2022-12-13T22:13:32Z

Done! branch is now main

Kevin-Mattheus-Moerman · 2022-12-13T22:13:46Z

@editorialbot generate pdf

editorialbot · 2022-12-13T22:15:32Z

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

Kevin-Mattheus-Moerman · 2022-12-13T22:17:34Z

@editorialbot accept

editorialbot · 2022-12-13T22:17:35Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2022-12-13T22:19:29Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-12-13T22:19:30Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2022-12-13T22:19:30Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04707 joss-papers#3803
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04707
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2022-12-13T23:11:09Z

Congratulations @robchallen on this JOSS publication!

Thank you @ajstewartlang for editing!!!

And a special thanks to the reviewers @debruine and @craig-willis !!!

editorialbot · 2022-12-13T23:11:10Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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reStructuredText:
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robchallen · 2022-12-16T16:04:21Z

Many thanks for all the input @craig-willis @debruine @Kevin-Mattheus-Moerman @ajstewartlang. Very pleased to get this out. Have a great Xmas!

editorialbot added R review labels Aug 24, 2022

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[PRE REVIEW]: dtrackr: An R package for tracking the provenance of data #4525

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JOSS Review terminological/dtrackr#16

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[REVIEW]: dtrackr: An R package for tracking the provenance of data #4707

[REVIEW]: dtrackr: An R package for tracking the provenance of data #4707

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[REVIEW]: dtrackr: An R package for tracking the provenance of data #4707

[REVIEW]: dtrackr: An R package for tracking the provenance of data #4707

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Software paper

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Software paper

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