EXPLORING HOW TO SET UP AN OPEN LAB BOOK
First things first
Since this is my first post attempting to use a reproducible workflow integrated with the “rmarkdown” package and “knitr” as well as “git”, “github” and maybe “jekyll”, this first part of the post covers how to install these.
install R studio
installing Rmarkdown package to create write the document
setting up a github account
http://www.github.com - click “create account”
downloading git for windows and setting up https connection
guide to install git for windows http://guides.beanstalkapp.com/version-control/git-on-windows.html
set username and password https://help.github.com/articles/set-up-git/
caching your password in git https://help.github.com/articles/caching-your-github-password-in-git/
the most simple https-based github commands
cloning - fetching - merging - pulling https://help.github.com/articles/which-remote-url-should-i-use/
Jekyll and ruby installation guide
Jekyll install fix - change https to http
setting up the jekyll-bootstrap blog
IMPORTANT - figure out whether you are on https or ssh with github.
switching jekyll-bootstrap theme
See the themes here: http://themes.jekyllbootstrap.com/
I chose the mark-reid theme with the following lines in the git bash prompt in the root of my github site directory
Rake theme:install git="https://github.com/jekyllbootstrap/theme-mark-reid.git" > Enter "y" or "yes"
and this is the result
converting rmarkdown to markdown
This approach is necessary for Github Pages since plugins are not supported. Using this approach, we can convert the R Mardown file to plain Markdown using the R script below. The converted Markdown file will be saved in the same directory so that Jekyll can then convert the resulting file. For simplicity, I place the rmarkdown.r function in the root directory of my site (alternatively you can place this in your .Rprofile file in your home directory). I then call rmd.sh (also located in the root directory) to first, determine the directory where the script is be executed from, and two, call the convertRMarkdown function. This function will process all R Markdown files (.rmd by default) in the current working directory (which can be set explicitly with the dir parameter or by the rmd.sh script) and convert them to plain markdown (with .markdown file extension by default). Once converted, Jekyll will the process the resulting file(s). This file can be downloaded here.