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 mqwilber@gmail.com for more information.
Schedule
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 |
Etherpad: https://swcarpentry.etherpad.mozilla.org/2015-04-17-ucsb.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Setup
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
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.
Windows
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.
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.
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 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:
- Download the Software Carpentry Windows installer.
- Double click on the file to run it.
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. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
Windows
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.
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.