R: in Rstudio How to Make Knitr Output to a Different Folder to Avoid Cluttering Up My Drive

R: In RStudio how do I make knitr output to a different folder to avoid cluttering up my drive?

As Eric pointed out in the comments, if you're willing to forego the convenience of the Knit HTML button (which produces HTML files that live alongside your .Rmd), you can just call rmarkdown::render directly.

However, if you really need to customize your workflow, you can override the Knit HTML button to run whatever command you via the rstudio.markdownToHTML option. This command could invoke rmarkdown with specific options (such as output directory) and perform other pre- or post-processing tasks. Documentation here:

https://support.rstudio.com/hc/en-us/articles/200552186-Customizing-Markdown-Rendering

Note that setting the rstudio.markdownToHTML option will turn off some of the newer RMarkdown V2 integration features baked into RStudio, since RStudio will no longer be able to infer what engine is being used to render the document.

Rmarkdown directing output file into a directory

You could try setting the out_dir variable in the function you are giving knit to render:

knit: (function(inputFile, encoding) { 
      out_dir <- 'test';
      rmarkdown::render(inputFile,
                        encoding=encoding, 
                        output_file=file.path(dirname(inputFile), out_dir, 'analysis.html')) })

In RStudio, where is knitr markdown output located?

Under certain conditions, RStudio moves the knitted (HTML or PDF) file to a temporary directory (located under tempdir()). These conditions are:

• You are in a RStudio Project.
• The "Project build tools" are set to "Package".
• The RMD file is located in a subdirectory vignettes.
• Knitting is initiated with the "Knit" button in RStudio.

Typically, this happens when knitting a package vignette and has the purpose of "keep[ing] your vignettes folder from becoming cluttered with HTML files".

Changing the Project build tools, changing the folder name or closing the project prevents this behavior. Another way to keep the generated (HTML or PDF) file is to call rmarkdown::render interactively (although this is not exactly equivalent to the "Knit" button).

Note that this only affects where the generated file will be saved. The Working Directory while knitting is unaffected.

Is it possible to knit an R Markdown file only to a preview window/pane in RStudio without saving an html file?

I don't know of a way to attach this to the knit button, but you could write a function that does this:

• get the current file open in the edit pane. This answer gives details on that.
• run rmarkdown::render() with the output_dir argument set the way you want.

You can attach this function to a keyboard shortcut in RStudio using these instructions.

Here's a simple version of the function:

  knit2 <- function(filename = rstudioapi::getSourceEditorContext()$path,
                    output_dir = tempdir()) {
    result <- rmarkdown::render(filename, output_dir = output_dir)
    getOption("viewer")(result)
  }

Simply call knit2(), and the output will be written to tempdir(), which means the preview will appear in the Viewer pane. If you want it to write to "results", call it as

knit2(output_dir = "results")

If that's not a subdirectory of tempdir(), the preview will appear in an external browser.

Save R output to a different directory

You have a file argument in your write* function. If your Output directory is in your working directory, it works like this:

write.xlsx(df, file = "Output/table.xlsx")
write.csv(df, file = "Output/table.csv")

Dynamically naming the output file in a custom R-markdown function

If the fields that you want to use don't include R expressions, you can use yaml_front_matter() to extract their values and use those to construct the name for the output file:

---
title: "Untitled"
author: "Jane Doe"
date: "18/02/2022"
output: word_document
knit: >
  (function(input_file, encoding) {
    metadata <- rmarkdown::yaml_front_matter(input_file)
    output_file <- with(metadata, paste(title, "by", author))
    rmarkdown::render(input = input_file, output_file = output_file)
  })
---

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If your fields do include R expressions, this becomes a little more involved. You can apply the same principle, but now instead of getting the front matter from the RMarkdown file, you get it from the intermediate Markdown file generated during the rendering process. Then rename the result.

That could look something like this:

---
title: "Untitled"
author: "Jane Doe"
date: "`r Sys.Date()`"
output: word_document
knit: >
  (function(input_file, encoding) {
    # Render, keeping intermediate files for extracting front matter
    md_dir <- tempdir()
    output_file_temp <- rmarkdown::render(
      input = input_file,
      output_file = tempfile(),
      intermediates_dir = md_dir,
      clean = FALSE
    )
    
    # Get the rendered front matter from the intermediate Markdown file
    md_file <- fs::path_ext_set(fs::path_file(input_file), ".knit.md")
    metadata <- rmarkdown::yaml_front_matter(fs::path(md_dir, md_file))
    
    # Build the output file name based on rendered metadata
    output_name <- with(metadata, paste(title, "by", author, "on", date))

    # Add the file extension and move to the working directory
    output_ext <- fs::path_ext(output_file_temp)
    output_file <- fs::path_ext_set(output_name, output_ext)
    fs::file_move(output_file_temp, output_file)

    message("Output moved to: ", output_file)
  })
---

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