[REVIEW]: rdataretriever: An R package for downloading, cleaning, and installing publicly available datasets

[whedon]

Submitting author: @henrykironde (henry senyondo)
Repository: https://github.com/ropensci/rdataretriever
Version: v3.0.1
Editor: @fboehm
Reviewer: @RMHogervorst, @jsgalan
Archive: 10.5281/zenodo.4314115

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/1a121f31d1ef48bcef1c971539888ea0/status.svg)](https://joss.theoj.org/papers/1a121f31d1ef48bcef1c971539888ea0)

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

@RMHogervorst & @jsgalan, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @RMHogervorst

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 repository url?
• 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 (@henrykironde) 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @jsgalan

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 repository url?
• 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 (@henrykironde) 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @RMHogervorst, @jsgalan it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

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For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

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

OK DOIs

- 10.1371/journal.pone.0065848 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[fboehm]

@jsgalan and @RMHogervorst - please check boxes above as you complete your review. For any boxes that you can't check right now, due to needed edits or fixes, please discuss the issues here or open issues in the submission repository. And please let me know if you have any questions. Thank you again!

[RMHogervorst]

@henrykironde some notes about the JOSS paper:

The description in Statement of need is really beautiful and only after reading that part I finally understood what the problem is that this package is solving. I really really wish you'd include something like that in the Readme (and maybe Description) too.

REQUIRED:

• Add citations so that the references work in the text.
• I am asked to review a State of the field: Do the authors describe how this software compares to other commonly-used packages? However I don't see that in the paper at this moment. Could you add something about the state of the field? I don't know what the state of the art is at this moment for the field, but I imagine workflow tools like Drake are used? What is the current state of automation/datapreparation? Is everyone using home brewed scripts? I am genuinely curious.

OPTIONAL / SUGGESTIONS:

• I am not very knowledgeable of the world of ecology or environmental sciences but the concept of frictionless data was new for me. Maybe add one sentence about what that entails?

[RMHogervorst]

Required Issues opened:

• Make more clear to R-users what the value of this package is ropensci/rdataretriever#261 "make value more clear"
• vignette ropensci/rdataretriever#260 "vignette incomplete"
• Clarify OSI licence ropensci/rdataretriever#257 "clarify OSI licence"

Optional issues opened:

• suggestion remotes::install_github in stead of devtools::install_github ropensci/rdataretriever#259 "suggestion for remotes in stead of devtools::install_github"
• [optional] is it necessary to download all the scripts to ~/.dataretriever ? ropensci/rdataretriever#262 "is it necessary to download all the scripts"
• Consider vignette of more examples ropensci/rdataretriever#263 "vignette of more examples"
• [optional] consider more explanation about commit ropensci/rdataretriever#264 "consider more explanation about commit"

[whedon]

👋 @RMHogervorst, please update us on how your review is going.

[whedon]

👋 @jsgalan, please update us on how your review is going.

[fboehm]

@jsgalan - I hope that the review is going well. As you work through the checklist above, please check the boxes to reflect your approval of the checklist items. Please let me know if there's something that I might do to assist you. Thanks again!

[henrykironde]

Just an update, @RMHogervorst made some great suggestions and I am working to resolve those. Thanks to the issues btw, I guess @jsgalan is inline with the issues raised.

[fboehm]

Thank you for the update, @henrykironde ! Please let me know how the resolution of issues goes, and don't hesitate to contact me when I might help with something.

[RMHogervorst]

Just an update: I feel @henrykironde and others are doing great work. I really look forward to the finished version!

[henrykironde]

Thanks folks. We have covered all the issues, I am happy to get more recommendations to consider.

[jsgalan]

Hi all, is there any confirmation I might be missing?

I am unable to check the ticks for the revision (Just checked in two distinct browsers to discard a software issue).

Thanks

Ps. has the invitation link expired? Attn: @fboehm

[jsgalan]

Hi all,

No problem in the Conda installation

But a problem was found in the R installation.

Did not found any description on the repository, are there any set requirements for the R installation?

Best

EDIT: I installed version 3.6.3 and everything installed correctly.

[jsgalan]

Hi all, It seems I was not in a top level repository.

All datasets are visible from Python

Had a bit of trouble to finally set up the Reticulate package but everything was set at the end (Extra information that helped https://docs.ropensci.org/rdataretriever/ , https://rstudio.github.io/reticulate/articles/versions.html and https://stackoverflow.com/questions/40788645/how-to-create-renviron-file)

All the tabular datasets and updates were collected correctly

[jsgalan]

Hi all,

I had problems installing the spatial datasets

Even though I have everything set up in Postgres

Any ideas?

Best

[henrykironde]

Thanks @jsgalan for testing this. Make sure you are creating the extensions in the same database that you want to install the data. The default is postgres. In case you, are using a different database, please try to provide the database name in the function call.
Let me know if that works

[jsgalan]

@whedon assign @jsgalan

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[jsgalan]

@whedon commands

[arfon]

@fboehm - this PR (ropensci/rdataretriever#283) should fix the paper compilation issue.

[ethanwhite]

I just merged @arfon's PR.

[arfon]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2800 with the following error:

/app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in parse': (6745a8ccdad111558cf0a673/paper/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in parse_stream'
from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:390:in parse' from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:277:in load'
from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:578:in block in load_file' from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in open'
from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in load_file' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/lib/whedon.rb:127:in load_yaml'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/lib/whedon.rb:87:in initialize' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/lib/whedon/processor.rb:38:in new'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/lib/whedon/processor.rb:38:in set_paper' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/bin/whedon:58:in prepare'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/bin/whedon:131:in <top (required)>' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `

'

[arfon]

Found one more issue: ropensci/rdataretriever#284

[ethanwhite]

Merged.

[arfon]

@whedon generate pdf

🤞third time's a charm?

[whedon]

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

[fboehm]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1371/journal.pone.0065848 is OK
- 10.21105/joss.00451 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1974

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1974, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

👋 @henrykironde - sorry that this slipped through the cracks. I'll work on it now

[danielskatz]

👋 @henrykironde - please update the metadata in the zenodo archive so that the title matches the title of the paper, and similarly, that the authors match the papers authors (both names and order)

[danielskatz]

I've proofread the paper and it looks good - it's ready to accept once the zenodo metadata fixes are made.

[arfon]

@henrykironde - just a reminder that we're waiting on your response here.

[henrykironde]

Going to get back to you asap

[henrykironde]

@arfon I think all issue are set, let me know incase something comes up.

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02800 joss-papers#2014
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02800
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@RMHogervorst, @jsgalan - many thanks for your reviews here and to @fboehm for editing this submission. JOSS relies upon the volunteer efforts of folks like yourselves - we simply wouldn't be able to do this without you ✨!

@henrykironde - your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02800/status.svg)](https://doi.org/10.21105/joss.02800)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02800/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02800/status.svg
   :target: https://doi.org/10.21105/joss.02800

This is how it will look in your documentation:

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