Update 20-r-rstudio.Rmd

[mblue9]

Change folder name they're told to create so it doesn't clash with repo folder.

@lgatto I'm testing for Smorgasbord and with Alex's setup the repo folder is imported, so the users will be starting with a bioc-intro folder in their working directory (same for bioc-rnaseq and bioc-project lessons). We could not add it but was thinking it might be good as anyone who wants to can see/run the episodes Rmds, data files etc, or if they have trouble with writing the code themselves they have access to code & data that runs. But need to change the name of the folder they're told to create here (bioc-intro) to not clash. Suggesting my-bioc-intro but could be something else.

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[lgatto]

• I don't mind implementing the proposed change, as it doesn't fundamentally modify the teaching.

• I understand that it can be useful to provide files with the code (only) or the Rmds to save participants some typing (although, I do think the typing is part of the learning), but I am wondering if letting them grep the whole repo isn't a bit confusing because there's much more in there. It should be possible to bundle the Rmd and tangled R code into a single zip file for download. Would that be useful?

[mblue9]

I understand that it can be useful to provide files with the code (only) or the Rmds to save participants some typing (although, I do think the typing is part of the learning), but I am wondering if letting them grep the whole repo isn't a bit confusing because there's much more in there. It should be possible to bundle the Rmd and tangled R code into a single zip file for download. Would that be useful?

Agree, not overwhelming them with unimportant (to them) files would be good. So for Smorgasbord we could see if we could provide just the episodes folder as a zip which has the Rmds, the data and figures, so that the data files are there as backup in case of any issues downloading, and they have all they need to render the Rmds if they want?

[lgatto]

@zkamvar - what would be the best way to automatically create artefacts when rendering the site?

[lgatto]

We discussed this during our bioc-teaching meeting and I was pointed to the Download handouts button. This is what we need and I'll investigate.

[zkamvar]

Two things:

1. all rendered output is rendered and flattened to the md-outputs branch
2. The handout for lessons is currently enabled by adding an option before the build process (see R-ecology-lesson sandpaper-main.yaml#L60). You can add or remove code cunks by using purl = TRUE.
3. I'm working on a method of generally enabling handouts from the config, but there is still some tweaking to be done: Enable handouts without using knitr::purl() carpentries/pegboard#101
4. I'm bad at counting, so I use computers to do it for me

[lgatto]

@mblue9 - could you look at the latest/current version of the course. There's now a Download handouts button to get a single large R script with all the code chunks.

• Does this solve the need?
• Assuming the answer to the above point is yes, is the current PR still relevant?
• Note that we could also provide the section Rmd - would this be useful in addition to the R scipt?

[mblue9]

That download button is very nice. Not sure that Rmd is needed so we could just go with script for now. I'll close this.