Reproducible Research Workshop
Table of Contents
May 13, 2015 12:30-4:30 PM, Biology 405
Setup
The windows computers in room 405 will have software pre-installed. If you want to bring your own laptop (recommended), please install the following software.
The Bash Shell
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
- Windows
Install Git for Windows by download and running the installer this will provide you with both Git and Bash in the Git Bash program.
- Mac OS X
The default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in
/Applications/Utilities
). You may want to keep Terminal in your dock for this workshop. - Linux
The default shell is usually
bash
, but if your machine is set up differently you can run it by opening a terminal and typingbash
. There is no need to install anything.
Git
Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. I recommend you go ahead now and obtain a github.com account. This is not necessary, but will allow you to store your repositories on github for collaboration.
- Windows
Git should be installed on your computer as part of your Bash install (described above).
- Mac OS X
For OS X 10.9 and higher, install Git for Mac by downloading and running the installer. After installing Git, there will not be anything in your
/Applications
, as Git is a command line program.For older versions of OS X (10.6-10.8) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.8.
- Linux
If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git
and for Fedora runsudo yum install git
.
R
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we'll use RStudio.
- Windows
Install R by downloading and running this .exe file CRAN. Also, please install the RStudio IDE.
- Mac OS X
Install R by downloading and running this .pkg file CRAN. Also, please install the RStudio IDE.
- Linux
You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run
sudo apt-get install r-base
and for Fedora runsudo yum install R
. Also, please install the RStudio IDE.
Course Materials
- Etherpad: we'll use this etherpad to share notes and code: https://etherpad.mozilla.org/2015-05-13-rr-workshop
- Lecture notes