Rmarkdown directing output file into a directory

Question

I found a really nice trick (link) to a function of knitr, where you can save your output html into an output folder and under a different filename.

The only thing you have to head to the header is the following:

title: "analysis"
author: "Me"
date: "`r format(Sys.time(), '%d %B, %Y, %H:%M')`"
knit: (function(inputFile, encoding) { 
      rmarkdown::render(inputFile,
                        encoding=encoding, 
                        output_file=file.path(dirname(inputFile), out_dir, 'analysis.html')) })
output:
  html_document:
    number_sections: yes
    toc: yes

This works on my Mac 'sometimes' very well, but sometimes it has problems to find the out_dir variable...

I first thought about executing the chunks first, so the variable is set... But this didn't solved the problem...

I also restarted R session and this didn't helped.

The last step was closing R, saving the workspace and after reopening R and loading workspace it works like a charm again.

I could not find the original post, where somebody recommended this trick...

EXACT WORKFLOW TO REPRODUCE

open new project, name it test in a new folder
create a r markdown document
change the header to:

---
title: "Untitled"
author: "Me"
date: "`r format(Sys.time(), '%d %B, %Y, %H:%M')`"
knit: (function(inputFile, encoding) { 
      rmarkdown::render(inputFile,
                        encoding=encoding, 
                        output_file=file.path(dirname(inputFile), out_dir, 'analysis.html')) })
output:
  html_document:
    number_sections: yes
    toc: yes
---

```{r write quant output files}
out_dir <- 'test'
if(!file.exists(out_dir)) {
  dir.create(out_dir)
}
```

save the document as test.Rmd
click the knit button (html is now removed from the options of the button)
This will fail!

Close the project!
Click on save environment!

Open the Project and click knit!
Everything works.

execute rm(list=ls()) everything works afterwards again

Answer 1

I found it cumbersome to write the output-file name so I swapped the output_file to output_dir argument but kept the rest of the code. In this way my Rmarkdown is still knitted into a subdirectory but with the inputFile name. Also, if the directory does not exist, it is created

---
title: "title"
author: "gordon freeman"
date: "`r Sys.Date()`"

knit: (function(inputFile, encoding) {
      out_dir <- "reports";
      rmarkdown::render(inputFile,
                        encoding=encoding,
                        output_dir=file.path(dirname(inputFile), out_dir))})
---