This is code and text behind my (Owen Jones's) CEED Workshop site. The material is intended for a workshop called "The Era Of Big Data Hits Conservation" held on 15-19th June 2015 at the ARC Centre for Excellence in Environmental Decisions (CEED). The workshop covers lots of ground, and this is just a small part of it concerning the use of phylogenetic information in conservation.

The site is based on Hadley Wickham's site for his Advanced R Programming book.

The site is built using Jekyll, with a custom plugin to render .rmd files with knitr and pandoc. To create the site, you need:

• jekyll and s3_websiter gems: gem install jekyll s3_website
• pandoc
• knitr: install.packages("knitr")
• bookdown: 'install_github("hadley/bookdown")'
• Ruby - you probably already have this installed.

Add the following to your .gitignore file.

Temp.html

Temp.Rmd

*.Rproj

_site

##Copying and deploying this site (e.g. to create a similar one)

I assume you are using a Mac with OSX.

• Create a new repository, XXX, with a .gitignore file
• Create a new branch of XXX called gh-pages (i.e. have two branches named "master" and "gh-pages")
• Use the Github app to clone XXX to your computer.
• Place the contents of ceed in the XXX directory master branch.
• Open Terminal, navigate to your XXX directory, run 'jekyll serve' and watch as directory "_site" is created. It may take a few moments.
• Stop the jekyll server (ctrl-c)
• Move "_site" to the desktop.
• In GitGub app, switch to the gh-pages branch.
• Move the contents of "_site" to the XXX directory of the gh-pages branch.
• Commit and synchronise to GitGub.
• Your site should be visible at http://username.github.io/XXX