[REVIEW]: overviewR - Easily Explore Your Data in R

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@cosimameyer@samhforbes<!--end-editor-- Reviewers: @drmowinckels, @milenamilena Archive: 10.5281/zenodo.7097560

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/b161adf6c81cedb2bda1ae36b54c6ce0/status.svg)](https://joss.theoj.org/papers/b161adf6c81cedb2bda1ae36b54c6ce0)

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

@drmowinckels & @milenamilena, 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 @samhforbes 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

📝 Checklist for @drmowinckels

📝 Checklist for @milenamilena

editorialbot commented 1 year ago

Hello humans, 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 commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (988.6 files/s, 218182.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            34           1727            470           9116
R                               25            226            581           1975
Markdown                         6            369              0           1349
Rmd                              4            319            857            429
CSS                              3             99             48            428
JavaScript                       4             64             34            266
YAML                             7             35              6            237
TeX                              1             11              0            102
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                            85           2850           1997          13913
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1167

editorialbot commented 1 year ago

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

samhforbes commented 1 year ago

Hi @drmowinckels, @milenamilena, please see the instructions at the top of the review thread.

Once you've generated your checklist you can use this as the basis for your review. Generally speaking it's useful to post an overview here, but deal with individual points by opening issues on the target repository, and linking them here so we are all on the same page. Feel free to direct any queries to me, but otherwise we look forward to the benefit of your expertise.

drmowinckels commented 1 year ago

Review checklist for @drmowinckels

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/cosimameyer/overviewR?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@cosimameyer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

milenamilena commented 1 year ago

Review checklist for @milenamilena

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/cosimameyer/overviewR?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@cosimameyer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

cosimameyer commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

cosimameyer commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- None

INVALID DOIs

- None

cosimameyer commented 1 year ago

@milenamilena @drmowinckels Many thanks for your feedback so far - I highly appreciate your time and energy going into it! I incorporated your suggested changes that we have received so far and updated the PDF.

milenamilena commented 1 year ago

I have completed my review, and I found this package very useful and holistic in giving an overview of data. The functions are very clear and well explained. The latex tables were beneficial, as the format is very clear. I also found very interesting the use of the Venn diagram and the ability to customise some gglots. I agree with the comments made by @drmowinckels and am happy to see that they were addressed. It is very promising to see that there are open issues in the repository, mainly for further enhancement. The whole paper is very explanatory, even for a naive R user.

drmowinckels commented 1 year ago

I have completed my review and am happy with the responses and changes made to the package and paper. The package functionality is well documented and covers something that has no real alternative in the R eco-system as I know it. Its clearly well-thought out and tested, and the implementation is great.

@samhforbes I believe both reviewers are happy with the package and paper status.

samhforbes commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

samhforbes commented 1 year ago

Hi @milenamilena @drmowinckels thanks for your hard work and suggestions. We appreciate both your thoroughness and the time spent reviewing and improving packages for JOSS.

@cosimameyer it looks like things are all coming together!

There's a couple of things we need to do before ticking off the final box. So can you please:

Let me know the final version number (I think you are now on 0.0.11, don't know if you are planning to go to 12 before this is finished)
Can you create a tagged release and archive a JOSS accepted version somewhere with a DOI, and paste the DOI here

Thanks!

cosimameyer commented 1 year ago

Thanks for the update and for putting your time into it - it’s highly appreciated! This review process is one of the best I've experienced (not just because of the outcome 😉) I think the discussions here and in the issues as well as the general feedback you get are so valuable! So thanks to all you for volunteering at the journal and for sharing your expertise ☺️

@samhforbes here's the missing information:

We upgraded overviewR to 0.0.12 (can you upgrade it here? I'm not sure if I can do it myself)
I archived the GitHub repo at Zenodo, the DOI is 10.5281/zenodo.7075665

samhforbes commented 1 year ago

@cosimameyer Brilliant stuff - I'll make those changes here, and then I am satisfied we can recommend accept. Well done on a great package and paper.

samhforbes commented 1 year ago

@editorialbot set v0.0.12 as version

editorialbot commented 1 year ago

Done! version is now v0.0.12

samhforbes commented 1 year ago

@editorialbot set 10.5281/zenodo.7075665 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7075665

samhforbes commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

:warning: Error prepararing paper acceptance. The generated XML metadata file is invalid.

Element xref is not declared in institution list of possible children

editorialbot commented 1 year ago

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- Errored finding suggestions for "Moving beyond votes: Estimating and analyzing stat...", please try later
- Errored finding suggestions for "Power struggle and spark of hope: The political el...", please try later
- Errored finding suggestions for "naniar: Data Structures, Summaries, and Visualisat...", please try later

INVALID DOIs

- None

oliviaguest commented 1 year ago

@openjournals/joss-eics @openjournals/dev something mysterious is afoot! ☝️

oliviaguest commented 1 year ago

I would be surprised if it is the missing DOIs @cosimameyer that are causing that error, but no harm in fixing those while we wait. 😊

oliviaguest commented 1 year ago

@editorialbot check references

cosimameyer commented 1 year ago

@oliviaguest Thanks for following up! I'm not sure if it really is a missing DOI (I didn't change anything in the references). The first two were already part of our initial submission (and, as far as I know, they don't have a DOI) and the third one (naniar) was added as part of the review process - but I checked the references after making the changes here (https://github.com/openjournals/joss-reviews/issues/4740#issuecomment-1239705390) and the editorial bot did not complain. Let me know what you think 😊

editorialbot commented 1 year ago

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- Errored finding suggestions for "Moving beyond votes: Estimating and analyzing stat...", please try later
- Errored finding suggestions for "Draw Venn Diagram by ’ggplot2’", please try later
- Errored finding suggestions for "Convert Country Names and Country Codes", please try later
- Errored finding suggestions for "dplyr: A Grammar of Data Manipulation", please try later

INVALID DOIs

- None

xuanxu commented 1 year ago

For the references with missing DOIs @editorialbot tries to find suggestions using the Crossref API. That error message means Crossref server did not respond, so probably there's a problem in their side. The solution is just wait and retry later.

oliviaguest commented 1 year ago

OK, just try again later, @samhforbes. Thanks @xuanxu! ☺️

samhforbes commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- Errored finding suggestions for "Moving beyond votes: Estimating and analyzing stat...", please try later
- Errored finding suggestions for "Power struggle and spark of hope: The political el...", please try later
- Errored finding suggestions for "dlookr: Tools for Data Diagnosis, Exploration, Tra...", please try later
- Errored finding suggestions for "summarytools", please try later
- Errored finding suggestions for "Draw Venn Diagram by ’ggplot2’", please try later
- Errored finding suggestions for "Convert Country Names and Country Codes", please try later
- Errored finding suggestions for "ggplot2: Create Elegant Data Visualisations Using ...", please try later
- Errored finding suggestions for "dplyr: A Grammar of Data Manipulation", please try later
- Errored finding suggestions for "overviewR", please try later
- Errored finding suggestions for "Hmisc: Harrell Miscellaneous", please try later
- Errored finding suggestions for "gtsummary: Presentation-Ready Data Summary and Ana...", please try later
- Errored finding suggestions for "naniar: Data Structures, Summaries, and Visualisat...", please try later
- Errored finding suggestions for "skimr: Compact and Flexible Summaries of Data", please try later
- Errored finding suggestions for "DataExplorer: Automate Data Exploration and Treatm...", please try later

INVALID DOIs

- None

cosimameyer commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- None

INVALID DOIs

- None

cosimameyer commented 1 year ago

@samhforbes it worked 🎉

samhforbes commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

:warning: Error prepararing paper acceptance. The generated XML metadata file is invalid.

Element xref is not declared in institution list of possible children

editorialbot commented 1 year ago

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- None

INVALID DOIs

- None

cosimameyer commented 1 year ago

As far as I understand the log (and I might be completely off here), there is an invalid JATS. Is it the DOI that I provided that causes the problems? I'm not sure but I believe it should be fine. If there's anything that I can/should do, let me know 😊

danielskatz commented 1 year ago

@xuanxu - can you take a look at this?

samhforbes commented 1 year ago

Right Crossref seems to think all systems are operational so I'll have another go here.

samhforbes commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

:warning: Error prepararing paper acceptance. The generated XML metadata file is invalid.

Element xref is not declared in institution list of possible children

openjournals / joss-reviews