layout: post
title: “Blog with Knitr and Jekyll”
description: “”
category: r

tags: [knitr, jekyll, tutorial]

{% include JB/setup %}

The knitr package provides an easy way to embed
R code in a Jekyll-Bootstrap
blog post. The only required input is an R Markdown source file.
The name of the source file used to generate this post is 2012-07-03-knitr-jekyll.Rmd, available
here.
Steps taken to build this post are as follows:

Step 1

Create a Jekyll-Boostrap blog if you don't already have one.
A brief tutorial on building this blog is available
here.

Step 2

Open the R Console and process the source file:

KnitPost <- function(input, base.url = "/") {
    require(knitr)
    opts_knit$set(base.url = base.url)
    fig.path <- paste0("figs/", sub(".Rmd$", "", basename(input)), "/")
    opts_chunk$set(fig.path = fig.path)
    opts_chunk$set(fig.cap = "center")
    render_jekyll()
    knit(input, envir = parent.frame())
}
KnitPost("2012-07-03-knitr-jekyll.Rmd")

Step 3

Move the resulting image folder 2012-07-03-knitr-jekyll and Markdown file
2012-07-03-knitr-jekyll.md to the local
jfisher-usgs.github.com git repository.
The KnitPost function assumes that the image folder will be placed in a
figs
folder located at the root of the repository.

Step 4

Add the following CSS code to the
/assets/themes/twitter-2.0/css/bootstrap.min.css file to center images:

[alt=center] {
  display: block;
  margin: auto;
}

That's it.

Here are a few examples of embedding R code:

summary(cars)

##      speed           dist    
##  Min.   : 4.0   Min.   :  2  
##  1st Qu.:12.0   1st Qu.: 26  
##  Median :15.0   Median : 36  
##  Mean   :15.4   Mean   : 43  
##  3rd Qu.:19.0   3rd Qu.: 56  
##  Max.   :25.0   Max.   :120  

par(mar = c(4, 4, 0.1, 0.1), omi = c(0, 0, 0, 0))
plot(cars)

Figure 1: Caption

par(mar = c(2.5, 2.5, 0.5, 0.1), omi = c(0, 0, 0, 0))
filled.contour(volcano)

Figure 2: Caption

And don't forget your session information for proper reproducible research.

sessionInfo()

## R version 2.15.1 (2012-06-22)
## Platform: x86_64-pc-mingw32/x64 (64-bit)
## 
## locale:
## [1] LC_COLLATE=Korean_Korea.949  LC_CTYPE=Korean_Korea.949   
## [3] LC_MONETARY=Korean_Korea.949 LC_NUMERIC=C                
## [5] LC_TIME=Korean_Korea.949    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] knitr_0.6.3
## 
## loaded via a namespace (and not attached):
## [1] digest_0.5.2   evaluate_0.4.2 formatR_0.5    plyr_1.7.1    
## [5] stringr_0.6    tools_2.15.1