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 typing bash. 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 run sudo 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 run sudo yum install R. Also, please install the RStudio IDE.

Course Materials

External resources

R and RStudio

Markdown

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