Loving Markdown!

Ok, so for those who don't know, the guys from RStudio recently teamed up with Yihui to add some really nice report authoring options in RStudio using the packages knitr ability to turn a combination of markdown and R code into html.

I have to admit, this has really changed how I work. Previously, I generally had R scripts, that I would then run, and summarize the results in a separate document as a report on what I had done. I know, many like to talk about Sweave, the language that R uses to generate vignettes demonstrating package functionality, but have you ever tried to write a Sweave document?

You need to know a fair amount about Latex, and even then it can be difficult to get the output you want. In addition, reading the raw file can be quite painful (I know, I have my own Bioconductor package that I wrote a Sweave vignette for).

Writing R Markdown documents just feels different. When I read the raw source of a Markdown document, I can actually read it, code and all. What is really sweet is that instead of writing about what I am doing in the comments, I write it out in full in the document, and then have the code blocks doing the actual calculations. What is really great is to regenerate the report, I simply re-knit it to generate a new html file.

It is so much easier to work with, that I am probably going to switch even how I write my blog posts, using a Markdown document as the source. For right now, that means writing a .md file, and then converting it to html using the R Markdown package, and then writing in the html to Blogger. You can see a good explanation of that process from Jeffrey Horner's blog here and here.

When I combine this with a github repo for storage, it also means I have some other place to keep the raw source of my blog posts, as well as easily read and edit the text. For example, you can read the raw text that was used for this post.

Source of this post is at https://github.com/rmflight/blogPosts/blob/master/rmarkdown_post_150812.md. Published at http://robertmflight.blogspot.com/2012/08/loving-markdown.html