Support spinning of R scripts

[holgerbrandl]

A great way to render reports from R is via knitr::spin. See https://bookdown.org/yihui/rmarkdown-cookbook/spin.html for an overview.

I had previously supported a small utility to simplify spinning of R-scripts from a terminal via https://github.com/holgerbrandl/rendr directly written in R, but it always lacked beauty.

It would be great if quarto could support spinning via

quarto render my_script.R 

Currently, this fails with

λ quarto render exp_fit.R
ERROR: Unable to render exp_fit.R

Error: Unable to render exp_fit.R
    at fileExecutionEngineAndTarget (file:///C:/Program%20Files/Quarto/bin/quarto.js:57992:15)
    at renderFiles (file:///C:/Program%20Files/Quarto/bin/quarto.js:86443:52)

What's your take on that?

[mcanouil]

Simply use quarto run script.R.

[holgerbrandl]

Thanks @mcanouil . I've tried to do so, but for me this creates just a Rplots.pdf only, so it seems. that it's not spinning the script but rather doing something like R -f <script> internally.

[mcanouil]

Note that a Jupyter Notebook is not a Python script.
For instance, there is nothing that can convert a Python script into a Quarto document which would be the correct parallel with knitr::spin for R scripts.

Quarto's main focus is on writing content, thus R/Python scripts are not the best input for that in my opinion.
I never saw in the wild a manuscript written from an R script via the knitr::spin function.
It seems to be really a niche that can easily be address for simple markup via the updated command I shared.

[cderv]

@holgerbrandl wouldn't using your tool with quarto run provide some help ?

quarto run rend.R MyScript.R

Maybe with some tweaks.

I think what's being desired is an alternate format option to produce a .qmd file instead of a .Rmd file which would require change to knitr::spin?

@kylebutts I opened an issue with this suggestion:

• Support .qmd in knitr::spin() yihui/knitr#2284

[holgerbrandl]

Thanks for pushing the idea forward.

Regarding the use of rend.R. Being the author myself, nobody is offended when stating that rend.R is just a poor workaround to enable some bash method to render any R-script into a html (or whatever pandoc-supported) format. Having a more structured way would be certainly better compared to what

Adding qmd output support to knitr::spin seems a great idea to me. Where can I find a listing of format differences between .qmd and .Rmd? From what I read they seem quite similar at first glance. In my experience, users of spin rely quite a lot on chunk options for different section (e.g. to adjust image size), so it would be important to preserve this feature.

[cderv]

Now there is more broader issue to follow for this feature in Quarto

• Render a document from a script (.R, .py) #6660

We'll see what can be done.

[cderv]

Related to @kylebutts suggestion in #4969 (reply in thread), now knitr (from 1.44) supporting spin(format = "qmd", knit = FALSE) to transform a R script to a .qmd document.

See

• Support .qmd in knitr::spin() yihui/knitr#2284

[holgerbrandl]

Thanks for implementing it in v1.4. Just gave it a first try, and it works just great.