Using subdirectories with quarto and RStudio

user_6325531 0
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Please consider the following.

I like to structure my R projects with different subdirectories. Using bookdown or quarto seems to make this quite difficult since both like to have their source files (.Rmd or .qmd) in the project directory. I was hoping that this will get easier with quarto but this does not seem the case, although it should be possible according to this post.

Problem description (replicable example)

Start a new quarto book project in RStudio: File > New Project > New Directory > Quarto Book.

This will create several .qmd files in the R project directory. Now create new subdirectories. Starting from the R project directory: scripts/qmd.

If we put all .qmd files from the R project directory into scripts/qmd, we also need adapt their path in the _quarto.yml (e.g., from index.qmd to / scripts/qmd/index.qmd).

After doing so and pressing the Render button, we receive the ERROR: Book contents must include a home page (e.g. index.md).

Putting only the index.qmd file back into the R Project directory (and adapt the _quarto.yml), the book can be rendered.

Question

  • How can we put all .qmd files into a dedicated subdirectory?

Edit (ignore below)

Originally the below question was also asked but is now answered: quarto does not seem to have a "merge-knit" option like bookdown (see here). This unfortunately makes quarto useless for my use case.

  • If this is not possible, how can we make sure that object created in the R project directory are accessible for the .qmd files in the subdirectories? (setting execute-dir: project as suggested here did not work for me.
quarto bookdown r
2 Answers

I'm assuming your purpose is just a specific personal preference for file organization.

You can have a large portion of your content in subdirectories (and that's my understanding of what Alison's blog post refers to), but you still need to have your index.qmd in the root. For example, you can have a subdirectory for projects, another one for posts, another one for tutorials, like Alison does.

In any case, one way of achieving what you want is by using pre- and post-render scripts.

You could move all the files from the scripts/qmd directory before rendering and then move them all back afterwards.

  pre-render: mv scripts/qmd/*.qmd .
  post-render: mv *.qmd scripts/qmd

Incidentally, that doesn't match my own personal preference ;-)

user_18505610

@Lucas A. Meyer, I tested the pre-render and post render options you suggested above, however, it throws an error after moving the file from my subdirectory to the project root: ERROR: NotFound: The system cannot find the file specified. (os error 2)

Then, it fails to render the file and move it back to the original subdirectory location.

I then set execute-dir: project in my .yml file thinking it was trying to execute in the wrong folder, but it did not change anything.

P.S. I would have added as a comment, but my reputation is not high enough, yet. :(

UPDATE1: I thinking I found a workaround for the time being. I've include the following project options beneath the project: header:

output-dir: subdir1/subdir2 Moves the html file, only.
post-render: xcopy *_files subdir1/subdir2 /E Copies the supporting files over.

The mv shell command can't be used for directories or you get the Directory Not Empty error.`

user_128816270
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