{chunktop}

[Note: this didn't quite work out as I'd planned, so it's archived. Read more in the blogpost.]

Scenario: you’ve written a report in an R Markdown file, but your collaborator is not an R user. You want to transfer the content of an R Markdown chunk option to them for editing; perhaps something text heavy, like the ‘fig.cap’ option. They’ll return to you the edited text and you want to insert their changes back into the relevant chunk. This is John’s reality.

The goal of {chunktop} is to extract the values of selected chunk options, prepare them for external editing, receive the results and reinsert them into the original R Markdown file. It uses the {parsermd} package for all the heavy lifting.

Install from GitHub:

if (!require("chunktop")) {
  install.packages("remotes")
  remotes::install_github("matt-dray/chunktop")
}
# Loading required package: chunktop

Currently the package will read an Rmd file and extract specific chunk options to a list; convert this data to a data.frame to be saved to CSV; reads in that CSV to a data.frame; and converts it back to a list.

Here’s a demo R Markdown file and an Abstract Syntax Tree (AST) of its structure as extracted by {parsermd}.

path <- system.file("extdata/demo1.Rmd", package = "chunktop")
parsermd::parse_rmd(path)
# ├── YAML [1 lines]
# └── Heading [h1] - A header
#     ├── Chunk [r, 1 opt, 1 lines] - chunk1
#     └── Heading [h2] - A subheader
#         ├── Chunk [r, 2 opts, 1 lines] - chunk2
#         ├── Markdown [2 lines]
#         ├── Chunk [r, 1 lines] - chunk3
#         └── Chunk [r, 2 opts, 1 lines] - chunk4

Let’s use the {chunktop} functions to extract the options of interest.

(chunktop_list <- get_chunktop(path, c("fig.cap", "eval")))
# $chunk1
# $chunk1$eval
# [1] "FALSE"
# 
# 
# $chunk2
# $chunk2$fig.cap
# [1] "\"I am a fig caption.\""
# 
# 
# $chunk4
# $chunk4$fig.cap
# [1] "\"I am another fig caption.\""
# 
# $chunk4$eval
# [1] "TRUE"

(chunktop_df <- chunktop_to_df(chunktop_list))
#   chunk_name option_name                option_value
# 1     chunk1        eval                       FALSE
# 2     chunk2     fig.cap       "I am a fig caption."
# 3     chunk4     fig.cap "I am another fig caption."
# 4     chunk4        eval                        TRUE
  
csv_file <- tempfile(fileext = ".csv")

write.csv(chunktop_df, csv_file, row.names = FALSE)

(chunktop_df2 <- read.csv(csv_file))
#   chunk_name option_name                option_value
# 1     chunk1        eval                       FALSE
# 2     chunk2     fig.cap       "I am a fig caption."
# 3     chunk4     fig.cap "I am another fig caption."
# 4     chunk4        eval                        TRUE

(chunktop_list2 <- df_to_chunktop(chunktop_df2))
# $chunk1
# $chunk1$eval
# [1] "FALSE"
# 
# 
# $chunk2
# $chunk2$fig.cap
# [1] "\"I am a fig caption.\""
# 
# 
# $chunk4
# $chunk4$fig.cap
# [1] "\"I am another fig caption.\""
# 
# $chunk4$eval
# [1] "TRUE"

(chunktop_df3 <- chunktop_to_df(chunktop_list2))
#   chunk_name option_name                option_value
# 1     chunk1        eval                       FALSE
# 2     chunk2     fig.cap       "I am a fig caption."
# 3     chunk4     fig.cap "I am another fig caption."
# 4     chunk4        eval                        TRUE