(Semi-)automating the R markdown to blogger workflow

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In his recent post 100 most read R posts for 2012 (stats from R-bloggers) – big data, visualization, data manipulation, and other languages Tal Galili – the guy behind R-Bloggers – presents his wishlist for 2013. Among other things he states

“The next step will be to have a “publish to your WordPress/blogger” button right from the RStudio console – allowing for the smoothest R blogging experience one could dream of.

I hope we’ll see this as early as possible in 2013.”

Given that I had some troubles myself recently with finding a convenient way of creating post for this blog (a blogspot site) and that I didn't want to wait until RStudio may integrate such functionality, I decided to come up with my own work around for the time being.

But let's start from the beginning:

What I want:

  • I want to blog
  • I want to blog using RStudio's R markdown framework (as it is very convenient)
  • I want to have code highlighting in my posts

What I don't want:

  • I don't want to manually fiddle around in the html code for each of the posts I create with RStudio
  • I don't want write blog posts using the compose section on blogger
  • Basically, I don't want to spend a lot of time on formatting (I rather spend the time on coding)

Why I want this:

  • For starters, because I'm lazy
  • Secondly, I want to integrate blogging into my teaching in the near future and for that I need a convenient and straight forward solution on how to create nice posts (after all I want to teach the students how to use R, not html)

The solution (as of now) is as follows (at least for me):

Yihui Xie has produced a SyntaxHighlighter Brush for the R Language which can be used for highlighting R code in blog posts.

In order to get the SyntaxHighlighter working on your blog, simply follow this tutorial at thebiobucket*.

However, the SyntaxHighlighter by Alex Gorbatchev, and subsequently also Yihui's brush for R, works a little different from the knitr code highlighting implementation. Basically, a chunk of code created with knitr is prepended by this little bit of html code:

<pre><code class="r"></code></p> <p>whereas SyntaxHighlighter requires the following format for it to work:</p> <p><code><pre class="brush: r"></code></p> <p>In order to automate the process of adjusting the brush definition needed for code highlighting using the SyntaxHighlighter brush I created the follwing function:</p> <pre>rmd2blogger <- function(rmdfile) { stopifnot(require(knitr)) ## knit rmdfile to <body> - only html knit2html(rmdfile, fragment.only = TRUE) ## read knitted html file htm.name <- gsub(".Rmd", ".html", rmdfile) tmp <- readLines(htm.name) ## substitue important parts tmp <- gsub("<pre><code class=\"r\">", "<pre class=\"brush: r\">", tmp) tmp <- gsub("</code></pre>", "</pre>", tmp) ## write with .blg file ending writeLines(tmp, paste(htm.name, ".blg", sep ="")) } </pre> <p><strong>This function has two important components to it:</strong></p> <ol> <li>it uses knitr's knit2html with <em>fragment.only</em> set to <em>TRUE</em>, which means your only creating the <code><body> part of the html.

  • it produces a .html.blg file in the path where the .Rmd is located where all syntax highlighting brushes are formatted to work with Yihui's R brush
  • To use it, simply provide the path to the .Rmd file you want to publish on your blogspot.


    Now, you can simply open the .html.blg file in a text editor and copy the complete contents into the html editor for a new post on your blogger site and the code R should look like the one above.

    In case you find any bugs, please let me know.

    ## R version 2.15.2 (2012-10-26)
    ## Platform: x86_64-pc-linux-gnu (64-bit)
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
    ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
    ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
    ##  [7] LC_PAPER=C                 LC_NAME=C                 
    ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
    ## attached base packages:
    ## [1] parallel  grid      stats     graphics  grDevices utils     datasets 
    ## [8] methods   base     
    ## other attached packages:
    ## [1] rgdal_0.7-25        raster_1.9-92       gridBase_0.4-6     
    ## [4] latticeExtra_0.6-19 lattice_0.20-10     RColorBrewer_1.0-5 
    ## [7] sp_0.9-99           knitr_0.9          
    ## loaded via a namespace (and not attached):
    ## [1] digest_0.6.0   evaluate_0.4.3 formatR_0.7    markdown_0.5.3
    ## [5] plyr_1.7.1     stringr_0.6    tools_2.15.2

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