Bradford Condon PhD

Bioinformatics, Web & Mobile Development


Knitting to Jekyll

Knitting R Markdown to Jekyll

This is a test of the Knittr package and Jekyll.

It looks like the original package for using knitr with Jekyll here has fallen out of favor for Hugo, a GO-based static web-site generator. Pretty cool, but let’s see how easy it is to knit into Jekyll without using any packages.

Load in some libraries and data

require(ggplot2)
require(knitr)
attach(mtcars)

Do some plots

head(mtcars)

##                    mpg cyl disp  hp drat    wt  qsec vs am gear carb
## Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
## Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
## Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
## Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
## Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
## Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1

qplot(mpg, drat, data=mtcars, color=cyl, main="mpg vs drat mtcars")

plot of chunk unnamed-chunk-2

Behold my beautiul plot!

Render

Next we need to get our RMD to MD, with the image paths sorted. To do this I’ll stand on the shoulders of chepec who has implemented a solution. I created a _knitr directory in my Jekyll site, and I included a knitr folder in my assets folder. Make sure you update the necessary paths in the render_post.r file.

Now its a matter of simply sourcing the file and running KnitPost. Make sure that your post titles match Jekyll requirements (start with YYYY-MM-DD format date). The result is a very rapid R-studio to web post!