Reproducible Research Course

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    

Internal links

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

Hosting on GitHub

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`.