Create RStudio_user.rst

[jcolomb]

Hello,

I have been noting my experience with datalad and R and Studio.

technical stuff seems to work now (including link in index).

Happy to talk about that during next week open hour.

• make indexing work
• test/modify boxes, links and images
• review content
• make links relative
• check whether to link/change some other part of the book according to these experience: created links and new issue Git-annex intro should introduce datalad drop and get #1041

[welcome]

(Image: CC-BY license, The Turing Way Community, & Scriberia. Zenodo. http://doi.org/10.5281/zenodo.3332808) Wohoo! 🎉 Thanks for opening your first pull request to the DataLad Handbook! 😎 We really appreciate your time and effort to contribute to the project - you're amazing! 👏

[adswa]

Thanks for the PR, @jcolomb! 🚀 Just as a short heads-up, I might not find time to take a look in detail this week, but I'm putting it on my project list for next week! ✔️

[jcolomb]

thanks, if you have time to look at it next Tuesday, we could present this to the office hours. I will also put this on hold until next week.

[adswa]

Sorry for the long delay here. I had to take a few weeks off to focus on my thesis, and this PR got lost over it.
I was wondering whether the content in this section can mirror what we have done with Jupyter Notebooks and DataLad run: We created a knowledge base item (https://knowledge-base.psychoinformatics.de/kbi/0003/index.html) and then linked it as further reading in the run chapter (https://handbook.datalad.org/en/latest/basics/101-113-summary.html#further-reading). I think this would be pretty optimal for this contribution to - it would only require minimal changes, and wouldn't need to fit into the handbook narrative as much as when integrated directly. And not everyone might be using R so those interested in it specifically can click the link (like for Jupyter). What do you think? If you agree, I can move your commit over to the knowledge base, and link it here.

Could you also make PR that adds your name, affiliation, and orcid to the .zenodo.json file (or leave the info as a comment here)? :)

hey @all-contributors please add @jcolomb for content

[allcontributors]

@adswa

I couldn't determine any contributions to add, did you specify any contributions?
Please make sure to use valid contribution names.

I couldn't determine any contributions to add, did you specify any contributions?
Please make sure to use valid contribution names.

I couldn't determine any contributions to add, did you specify any contributions?
Please make sure to use valid contribution names.

I've put up a pull request to add @jcolomb! 🎉

[jcolomb]

I also forgot about it, thanks for bringing it back in my working memory :)

I am inclined to think it would go better in the handbook, I am ready to put more work into it. (the datalad run part is only half of it, actually)

The handbook is the number one resource, the knowledge-base is not that user friendly... I do think an entry point for R and Rstudio users may be a good addition to the book.

I will try to clean and simplify the chapter, hopefully today. We can still move it somewhere else later if you think it would be better.

[jcolomb]

I reworked the first part, please tell me whether this would work better.
I would then work the rest of the use case, following a narrative we agree on.

thanks

[adswa]

Okay, I finally got around to starting the review! I have added a few suggestions for phrasing and markup right away. If you agree, you can just accept them.

I feel like the start of the usecase reads generally well, and it would be nice to make the part that starts with "HERE THE WRITING STOPS" fit into it - e.g., by sticking with the personas instead of "I"-form. My suggestion would be to add a section in a similar style focused on DataLad run and R scripts. This could help to limit the scope and shape out the section more clearly.

What would improve everything greatly, too, is to have real world screenshots of the RStudio GUI - for example from cloning a nested dataset from Gin, or saving something in a TONIC structured dataset, or executing a datalad command in its console.

What I'm unsure about are the sections that are about 'troubleshooting' or common questions. It feels maintenance intensive to duplicate this info - things that exist in the Basics part of the handbook should just be linked to (to not increase maintenance load - the more places a piece of info needs to be updated if it changes, the more work there is). And it might also create the impression that all of these infos are extras for RStudio, when they are actually general things. Maybe we can squeeze it into a list of bullet points with common questions and a link to where they are answered?

[adswa]

I feel like this can conclude with a statement that with this setup, everything is good to go for DataLad commands from the console, for example for saving changes,pushing modifications, pulling updates, or adding siblings.

[jcolomb]

Added some infos in the box, indeed pushing would need additional setups in the scenario

[adswa]

Maybe for this section it makes sense to focus it on the topic of reproducible execution with datalad run.
I think there is no need to spent too much work on rewriting content about the difference between files kept in git versus in git annex (instead, references to existing parts in the handbook).

[jcolomb]

I kept this in the following version because:

• beginners may not care about reproducible execution
• Infos about difference between Git and Git-annex is necessary to explain Rstudio behavior. I was personally very surprised of that behavior and needed testing and thinking to understand what happens. I try to add some reference for more info.

[jcolomb]

commit changes, will work on it offline and push a new version soon(ish). Thanks!

[jcolomb]

new version waiting for review :), some ref needs to be checked, I was not able to build locally.

[jcolomb]

figures working !! Will go through it again tomorrow and ask for final review :)

[jcolomb]

A bit later, but I think I got most of it right by now. I can't make internal links to work but for the first one.

[jcolomb]

End of year cleaning up... @adswa would you have time to see about these internal links and have a final check ? Would love to see this in the offical book by the end of the year :)

[adswa]

quick edits on the technical side

[adswa]

Could you merge the current main branch in your master branch? I'm seeing a weird build failure, and it might just be that the source has become a bit outdated

[jcolomb]

done.

[adswa]

alrighty, technical issues solved ✔️

[jcolomb]

two small changes, looks all good to me ! thanks a lot

[jcolomb]

Suggested change

	for data and for code, that were created using the `Tonic tool and templates <https://gin-tonic.netlify.app>`_ .
	for data and for code, that were created using the `Tonic tool and templates <https://gin-tonic.netlify.app>`_ , `see archived version <https://doi.org/10.5281/zenodo.7763694>`_ .

[jcolomb]

adding a link, so that if ever the website is put down, there is still a working link.

[jcolomb]

I think it could be merge ?

still some little issues, though

one link may be made relative at the end: https://handbook.datalad.org/en/latest/basics/101-108-run.html#run
figure numbering starts at 2
I put another suggestion to add one link.

@adswa anything else before merging ?

[jcolomb]

Hello,
sorry again I could not make it to the conference. Any plans for this PR, I would like to make room in my todo list :)

thanks for the work!

[jcolomb]

@adswa any news on this, would love to close it and free my mind :)

[jcolomb]

@adswa asking again, would like to have an official link for the end of the year report of our project.