Replace figure captions in r chunk headers in Rmd files with text captions

figcap_replace.R

# replace figure captions like:
# 
# ```{r myfigure, fig.cap = "This is my figure."}
#
# with text captions like this:
#
# (ref:myfigurelab) This is my figure.
#
# ```{r myfigure, fig.cap = "(ref:myfigurelab)"}

# https://bookdown.org/yihui/bookdown/markdown-extensions-by-bookdown.html#text-references

# get the files to search
files <- list.files(pattern = "\\.Rmd", full.names = TRUE)
names(files) <- basename(files)

# set the directory to save in (don't overwrite -- this is experimental)
newdir <- "new_Rmds"
if (!dir.exists(newdir)) dir.create(newdir)

# iterate over files
for (f in files) {
  # find r chunk lines with figure captions
  # only finds " captions, not ' -- fix this later
  lines <- readLines(f)
  figcaps <- which(grepl("^```\\{r.*fig\\.cap\\s*=\\s*\"[^ref:]", lines))
  figcaps <- rev(figcaps)

  for (l in figcaps) {
    # read a line with a figcap
    x <- lines[l]

    # extract the original fig.cap and chunk name
    orig_figcap <- stringr::str_extract(x, "fig\\.cap\\s*=\\s*\".+\"")
    chunkname <- stringr::str_extract(x, "^```\\{r,?\\s+[^(,| )]+")

    # make the label and new figure caption for the r chunk
    label <- gsub("^```\\{r,?\\s+", "", chunkname)
    label <- paste0(label, "lab")
    new_r_figcap <- paste0("fig.cap=\"(ref:", label, ")\"")

    # make the new r chunk header and caption
    new_r <- gsub(orig_figcap, new_r_figcap, x, fixed = TRUE)
    newcap <- gsub("fig\\.cap\\s*=\\s*\"", "", orig_figcap)
    newcap <- gsub("\"$", "", newcap)
    newcap <- paste0("(ref:", label, ") ", newcap)

    # replace the old r chunk header with the caption and new chunk header
    lines[l] <- paste0("\n\n", newcap, "\n\n", new_r)
  }

  # write new file
  write(lines, file.path(newdir, basename(f)))
}