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Convert Rmd document (knitr::knit) to an R script (knitr::spin) #RMarkdown #knitr #knit #spin
#' Backstitch an Rmd file to an R script
#'
#' Takes an Rmd file -- that would be converted with knitr::knit() -- and
#' "backstitches" it into an R script suitable for knitr::purl(). The output
#' file is the just the backstitched R script when `output_type = 'script'`, or
#' just the code chunks when `output_type = 'code'` (note that all inline code
#' is dropped in this case). Or finally, output both with
#' `output_type = 'both'`.
#'
#' You can load this function by calling:
#' devtools::source_gist('284671997992aefe295bed34bb53fde6', filename = 'backstitch.R')
#'
#' @param infile Input file name
#' @param outfile Output file name (`.R` extension added if not included)
#' @param ouput_type One of `script`, `code` or `both`. If `both`, two files are
#' created, with `_code` appended to the file name of the code chunks.
#' @param chunk_header Chunk header style, valid options are `"#-"`, `"#+"`, and `"# ----"`
backstitch <- function(
infile,
outfile = NULL,
output_type = c('both'),
chunk_header = "# ----"
) {
requireNamespace('knitr', quietly = TRUE)
requireNamespace('stringr', quietly = TRUE)
stopifnot(output_type %in% c('script', 'code', 'both'))
if (is.null(outfile) && output_type == 'both')
stop("Please choose output_type of 'script' or 'code' when not outputting to a file.")
knitr::knit_patterns$set(knitr::all_patterns[['md']])
x <- readLines(infile)
if (inherits(infile, 'connection')) close(infile)
empty_lines <- which(stringr::str_detect(x, "^\\s?+$"))
last_non_empty_line <- max(setdiff(seq_along(x), empty_lines))
x <- x[1:last_non_empty_line]
x_type <- rep('text', length(x))
# Find YAML section
yaml_markers <- which(stringr::str_detect(x, "^[-.]{3}\\s*$"))
if (length(yaml_markers) > 2) {
message("Input file may have multiple YAML chunks, only considering lines",
paste(yaml_markers[1:2], collapse='-'), 'as YAML header.')
}
if (length(yaml_markers) > 0) {
i.yaml <- yaml_markers[1]:yaml_markers[2]
x_type[i.yaml] <- 'yaml'
}
# Mark code chunk.begin, chunk.end and regular chunk codelines
i.chunk.begin <- which(stringr::str_detect(x, knitr::knit_patterns$get('chunk.begin')))
i.chunk.end <- which(stringr::str_detect(x, knitr::knit_patterns$get('chunk.end')))
x_type[i.chunk.end] <- 'chunk.end'
for (j in i.chunk.begin) {
j.chunk.end <- min(i.chunk.end[i.chunk.end > j])-1
x_type[j:j.chunk.end] <- 'chunk'
}
x_type[i.chunk.begin] <- 'chunk.begin'
# Check for inline code
i.inline <- which(stringr::str_detect(x, knitr::knit_patterns$get('inline.code')))
i.inline <- intersect(i.inline, which(x_type == 'text'))
x_type[i.inline] <- 'inline'
# Check empty lines
i.empty <- which(stringr::str_detect(x, "^\\s*$"))
i.empty <- intersect(i.empty, which(x_type == 'text'))
x_type[i.empty] <- 'empty'
really_empty <- function(x_type, j, n = -1) {
if (grepl('(chunk|yaml)', x_type[j + n])) {
return('empty')
} else if (n < 0) {
return(really_empty(x_type, j, 1))
} else if (x_type[j + n] %in% c('text', 'inline')) {
return('text')
} else {
return(really_empty(x_type, j, n+1))
}
}
for (j in i.empty) {
x_type[j] <- really_empty(x_type, j)
}
# Rewrite lines helper functions
comment <- function(x) paste("#'", x)
make_chunk_header <- function(x, chunk_header) {
stringr::str_replace(stringr::str_replace(x, knitr::knit_patterns$get('chunk.begin'), "\\1"),
"^r[, ]?", paste(chunk_header, ""))
}
# Rewrite lines
y <- x
regex_inline_grouped <- "`r[ ]?#?(([^`]+)\\s*)`"
i.empty <- which(x_type == 'empty')
i.text <- which(x_type == 'text')
y[i.chunk.begin] <- make_chunk_header(x[i.chunk.begin], chunk_header)
y[i.inline] <- comment(stringr::str_replace_all(x[i.inline], regex_inline_grouped, "{{\\1}}"))
y[i.text] <- comment(x[i.text])
if (length(yaml_markers) > 0) y[i.yaml] <- comment(x[i.yaml])
y[i.empty] <- ""
y[i.chunk.end] <- ""
y_code <- y[which(stringr::str_detect(x_type, 'chunk'))]
if (!is.null(outfile)){
outfile_name <- stringr::str_replace(outfile, "(.+)\\.R$", "\\1")
if (output_type == "script") {
cat(c(y, ""), file = paste0(outfile_name, ".R"), sep = '\n')
} else if (output_type == "code") {
cat(c(y_code, ""), file = paste0(outfile_name, ".R"), sep = '\n')
} else {
cat(c(y, ""), file = paste0(outfile_name, ".R"), sep = '\n')
cat(c(y_code, ""), file = paste0(outfile_name, "_code.R"), sep = '\n')
}
} else {
switch(
output_type,
'script' = unname(y),
'code' = unname(y_code)
)
}
}
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