RMarkdown render to Notebook with child chunks included - r

Question

I'm after a way to render an Rmd document (that contains references to various "child" files) to a self-contained R Notebook without these dependencies.
At the moment, the .Rmd code chunks are located throughout a number of .R, .py and .sql files and are referenced in the report using
```{r extraction, include=FALSE, cache=FALSE}
knitr::read_chunk("myscript.R")
```
followed by
```{r chunk_from_myscript}
```
as documented here.
I've done this to avoid code duplication and to allow for running the source files separately however these code chunks are only executable in the report via a call to knit or render (when read_chunk is run and the code chunk is available).
Is there a way to spin-off an Rmd (prior to knitting) with
just these chunks populated?
This function
rmarkdown::render("report.Rmd", clean = FALSE)
almost gets there as it leaves the markdown files behind whilst removing extraction and populating chunk_from_myscript however as these files are straight markdown, the chunks are no longer executable and the chunk options are missing. It obviously also doesn't include chunks where eval=TRUE, echo=FALSE which would be needed to run the resulting notebook.
I've also looked at knitr::spin however this would mean disseminating the contents of the report to every source file and isn't terribly ideal.
Reprex
report.Rmd
---
title: 'Report'
---
```{r read_chunks, include=FALSE, cache=FALSE}
knitr::read_chunk("myscript.R")
```
Some documentation
```{r chunk_from_myscript}
```
Some more documentation
```{r chunk_two_from_myscript, eval=TRUE, echo=FALSE}
```
myscript.R
#' # MyScript
#'
#' This is a valid R source file which is formatted
#' using the `knitr::spin` style comments and code
#' chunks.
#' The file's code can be used in large .Rmd reports by
#' extracting the various chunks using `knitr::read_chunk` or
#' it can be spun into its own small commented .Rmd report
#' using `knitr::spin`
# ---- chunk_from_myscript
sessionInfo()
#' This is the second chunk
# ---- chunk_two_from_myscript
1 + 1
Desired Output
notebook.Rmd
---
title: 'Report'
---
Some documentation
```{r chunk_from_myscript}
sessionInfo()
```
Some more documentation
```{r chunk_two_from_myscript, eval=TRUE, echo=FALSE}
1 + 1
```

Answer 1

Working through your reprex I now better understand the issue you are trying to solve. You can knit into an output.Rmd to merge your report and scripts into a single markdown file.
Instead of using knitr::read_chunk, I've read in with knitr::spin to cat the asis output into another .Rmd file. Also note the params$final flag to allow rendering the final document when set as TRUE or allowing the knit to an intermediate .Rmd as FALSE by default.
report.Rmd
---
title: "Report"
params:
final: false
---
```{r load_chunk, include=FALSE}
chunk <- knitr::spin(text = readLines("myscript.R"), report = FALSE, knit = params$final)
```
Some documentation
```{r print_chunk, results='asis', echo=FALSE}
cat(chunk, sep = "\n")
```
to produce the intermediate file:
rmarkdown::render("report.Rmd", "output.Rmd")
output.Rmd
---
title: "Report"
---
Some documentation
```{r chunk_from_myscript, echo=TRUE}
sessionInfo()
```
With the secondary output.Rmd, you could continue with my original response below to render to html_notebook so that the document may be shared without needing to regenerate but still containing the source R markdown file.
To render the final document from report.Rmd you can use:
rmarkdown::render("report.Rmd", params = list(final = TRUE))
Original response
You need to include additional arguments to your render statement.
rmarkdown::render(
input = "output.Rmd",
output_format = "html_notebook",
output_file = "output.nb.html"
)
When you open the .nb.html file in RStudio the embedded .Rmd will be viewable in the editing pane.

Answer 2

Since neither knitr::knit nor rmarkdown::render seem suited to rendering to R markdown, I've managed to somewhat work around this by dynamically inserting the chunk text into each empty chunk and writing that to a new file:
library(magrittr)
library(stringr)
# Find the line numbers of every empty code chunk
get_empty_chunk_line_nums <- function(file_text){
# Create an Nx2 matrix where the rows correspond
# to code chunks and the columns are start/end line nums
mat <- file_text %>%
grep(pattern = "^```") %>%
matrix(ncol = 2, byrow = TRUE)
# Return the chunk line numbers where the end line number
# immediately follows the starting line (ie. chunk is empty)
empty_chunks <- mat[,1] + 1 == mat[,2]
mat[empty_chunks, 1]
}
# Substitute each empty code chunk with the code from `read_chunk`
replace_chunk_code <- function(this_chunk_num) {
this_chunk <- file_text[this_chunk_num]
# Extract the chunk alias
chunk_name <- stringr::str_match(this_chunk, "^```\\{\\w+ (\\w+)")[2]
# Replace the closing "```" with "<chunk code>\n```"
chunk_code <- paste0(knitr:::knit_code$get(chunk_name), collapse = "\n")
file_text[this_chunk_num + 1] %<>% {paste(chunk_code, ., sep = "\n")}
file_text
}
render_to_rmd <- function(input_file, output_file, source_files) {
lapply(source_files, knitr::read_chunk)
file_text <- readLines(input_file)
empty_chunks <- get_empty_chunk_line_nums(file_text)
for (chunk_num in empty_chunks){
file_text <- replace_chunk_code(file_text, chunk_num)
}
writeLines(file_text, output_file)
}
source_files <- c("myscript.R")
render_to_rmd("report.Rmd", "output.Rmd", source_files)
This has the added benefits of preserving chunk options and working
with Python and SQL chunks too since there is no requirement to evaluate
any chunks in this step.