This is code and text behind the Reproducible Research Course taught by Eric C. Anderson of the National Marine Fisheries Service.

The site is built using jekyll, with a custom plugin (written by Hadley Wickham for his Advanced R programming book) to render .rmd files with knitr and pandoc. To create the site, you need:

• jekyll: gem install jekyll
• pandoc
• knitr: install.packages("knitr")
• rmarkdown install.packages("rmarkdown")
• bookdown Since I have my .rmd files in subdirectories I use a slightly modified version of this package that you can get thusly:
  devtools::install_github("eriqande/bookdown", ref = "index-recursively")

You should make sure that you have recent versions of the R packages. Here is what has worked for me:

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] knitr_1.6       bookdown_0.1    rmarkdown_0.3.3

loaded via a namespace (and not attached):
[1] digest_0.6.4    evaluate_0.5.3  formatR_0.10    htmltools_0.2.6 stringr_0.6.2   tools_3.1.0     yaml_2.1.11    

To link between sections, use internal links of the form #header-id. See some of the files.

I build this site locally, and I push the results up to the gh-pages branch. That involves some gymnastics that I will explain here once I figure it out. For now, to build it locally, just do ./build-site.sh. If you want to build it locally and have jekyll serve it up locally for you as well, do './build-site.sh -l`.