Create HTML page containing all package examples using knitr and markdown

January 23, 2013

(This article was first published on » R, and kindly contributed to R-bloggers)

Create HTML page containing all package examples using knitr and markdown

Yesterday, I was updating my website to include more information about some R packages I am working on. I wanted to create a page showing examples of the functionality that is available in each package. Now, I usually write a quite extensive amount of examples in the help pages, showing most of the functionality. A single page with the examples of each function in the package including the output would be a, although very simply, quite nice way to quickly demonstrate the functionality of the package.

This is not hard to do by hand. Simply copy the examples to an R markdown file, add knitr chunks and a title here and there and it should look good. But this seemed like something that would be nice to do every update, so I wanted to automate it. The results (which can be seen here and here) were quite nice, so I figured I maybe others could use these codes as well. Do keep in mind that these codes are hardly tested!

Below is the code for the function examplePage. It scans all of a packages .Rd files for an example section and extracts them. The function creates and compiles a markdown document with the following title levels:

  1. The package name (only at the top)
  2. The help-file name
  3. Any line in the example section that contain word characters and either starts with three or more #s or starts with an # and ends with an # or -.
  4. Any line that starts with (after spaces) exactly ##, followed by word characters and does not end on # or -.

These titles are chosen specifically such that the control-shift-R command in RStudio or something like #### BIG SECTION ####results in a large title.


examplePage has the following arguments:

  • pkg: Path to the package folder, should include a directory man with the Rd files.
  • openChunk: code to open chunks. Defaults to "{r, message=FALSE, warning = FALSE, error = FALSE}". This can be used to enter more knitr options.
  • includeDontshow: Logical stating if don't show environments should be included in the codes. Defaults to FALSE.
  • includeDontrun: Logical stating if don't run environments should be included in the codes. Defaults to TRUE.

The function:

examplePage <- function(pkg, openChunk = "```{r, message=FALSE, warning = FALSE, error = FALSE}", 
    includeDontshow = FALSE, includeDontrun = TRUE, exclude) {
    if (!require("knitr")) 
        stop("'knitr must be intalled.")
    if (!require("markdown")) 
        stop("'knitr must be intalled.")

    # Inner function to find closing brackets:
    findClose <- function(x, openLoc, open = "\\{", close = "\\}") {
        # Find close:
        nest <- 1
        i <- openLoc + 1
        repeat {
            # If open bracket in line:
            if (grepl(open, x[i])) {
                nest <- nest + length(gregexpr(open, x[i])[[1]])
            if (grepl(close, x[i])) {
                nest <- nest - length(gregexpr(close, x[i])[[1]])
            if (nest == 0) 
            i <- i + 1

    files <- list.files(paste0(pkg, "/man"), pattern = "\\.Rd$", = TRUE, 
        full.names = TRUE)

    # Exclude:
    if (!missing(exclude)) 
        files <- files[!grepl(exclude, files)]

    # Preparation:
    n <- length(files)
    subs <- character(n)

    # For each rd file:
    for (i in seq_along(files)) {
        # Read file:
        txt <- readLines(files[i])

        # Only include if there is only one example section:
        if (sum(grepl("\\\\examples\\{", txt)) == 1) {
            # Extract examples section:
            start <- grep("\\\\examples\\{", txt)
            end <- findClose(txt, start)
            txt <- txt[(start + 1):(end - 1)]

            # Don't show fields:
            dontshows <- grep("\\\\dontshow\\{", txt)
            if (length(dontshows) > 0) {
                ends <- numeric(length(dontshows))
                for (k in seq_along(dontshows)) {
                  ends[k] <- findClose(txt, dontshows[k])

                # Remove:
                if (includeDontshow) {
                  txt <- txt[-c(dontshows, ends)]
                } else txt <- txt[, mapply(dontshows, ends, FUN = ":", 
                  SIMPLIFY = FALSE))]

            # Don't run fields:
            dontruns <- grep("\\\\dontrun\\{", txt)
            if (length(dontruns) > 0) {
                ends <- numeric(length(dontruns))
                for (k in seq_along(dontruns)) {
                  ends[k] <- findClose(txt, dontruns[k])

                # Remove:
                if (includeDontrun) {
                  txt <- txt[-c(dontruns, ends)]
                } else txt <- txt[, mapply(dontruns, ends, FUN = ":", 
                  SIMPLIFY = FALSE))]

            # Enter main title and first R chunk:
            txt <- c(paste("##", gsub("\\.rd$", "", basename(files[i]), = TRUE)), 
                openChunk, txt, "```")

            # Crawl over lines. If a title is encountered, close chunk and replace
            # title with markdown:
            j <- 3
            repeat {
                # Small section (start with exactly two hashes, does not end with nonword:
                if (grepl("^\\s*##\\s*(\\w|\\s)+$", txt[j])) {
                  txt[j] <- gsub("^\\s*##\\s*", "#### ", txt[j])
                  txt <- c(txt[1:(j - 1)], "```", txt[j], openChunk, txt[(j + 
                  j <- j + 2

                  # Else large section, starts with #, ends with nonchar, or starts with
                  # more than 2 #'s
                } else if (grepl("\\w", txt[j]) & (grepl("^\\s*###", txt[j]) | 
                  grepl("^\\s*#.*[#-]\\s*$", txt[j]))) {
                  txt[j] <- gsub("^\\W*(?=\\w)", "### ", txt[j], perl = TRUE)
                  txt[j] <- gsub("(?<=\\w)\\W*$", "", txt[j], perl = TRUE)

                  txt <- c(txt[1:(j - 1)], "```", txt[j], openChunk, txt[(j + 
                  j <- j + 2
                } else if (grepl("^\\s*#\\W*$", txt[j])) {
                  # If start is comment and no words, remove:
                  txt <- txt[-j]
                  j <- j - 1

                j <- j + 1
                if (j > length(txt)) 

            emptySections <- which(txt[-length(txt)] == openChunk & txt[-1] == 
            if (length(emptySections) > 0) 
                txt <- txt[-c(emptySections, emptySections + 1)]

            txt <- gsub("\\\\%", "%", txt)
            subs[i] <- paste(txt, collapse = "\n")

    subs <- subs[order(nchar(subs), decreasing = TRUE)]
    subs <- c(paste0("# ", basename(pkg), "\n\n```{r,echo=FALSE,message=FALSE}\nlibrary(\"", 
        basename(pkg), "\")\n```"), subs)

    # Write Rmd:
    RmdFile <- paste0(basename(pkg), ".Rmd")
    write(paste(subs, collapse = "\n\n"), RmdFile)

    # Knit:
    mdFile <- gsub("Rmd", "md", RmdFile)
    knit(RmdFile, mdFile)

    # Markdown:
    htmlFile <- gsub("Rmd", "html", RmdFile)
    markdownToHTML(mdFile, htmlFile)



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