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University of California, Santa Barbara

Apr 17-18, 2015

9:00 am - 5:00 pm

Instructors: Mark Wilber, Tom Bell, Umi Hoshijima, Tom Smith, Louise Stevenson

Helpers: Max Castorani, Ana Elisa Garcia

General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Who: The course is aimed at graduate students and other researchers looking to use R as a research tool. The first day will cover R basics and the second day will cover version control and more advanced R topics.

Where: 1007 SSMS. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail for more information.


Day 1

8:30-9:00 Installation help (optional)
9:00-9:30 Introduction
9:30-10:45 The Shell
10:45-11:00 Coffee Break
11:00-12:30 Intro to R: The Basics I
12:30-1:30 Lunch
1:30-3:00 Intro to R: The Basics II
3:00-3:15 Coffee Break
3:15-4:45 Intro to R: Data, plots, and analysis
4:45-5:00 Wrap up

Day 2

9:00-10:45 More data, plots, and analysis and Version Control
10:45-11:00 Coffee Break
11:00-12:30 Special R Topics: ggplot and plyr
12:30-1:30 Lunch
1:30-2:30 Special R Topics: Big Data
2:30-2:45 Coffee Break
2:45-4:00 Special R Topics: Dynamic models
4:00-4:30 Wrap-up and discussion

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.


R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we will be using RStudio.


Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.

Mac OS X

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.


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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.


Install Git for Windows by downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Software Carpentry Windows Installer

It installs and configures nano (Among other things)

This installer requires an active internet connection.

After installing Git Bash:

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.


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 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 You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).


Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.


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.

Finally, install the Git GUI SourceTree which we will demo at the end of the Git lesson. SourceTree provides an easy way to interact with Git if you don't want to use the command line. This application is not available on Linux.