Software Carpentry with R at the UQ Winter School
11-12 July, 2016
9:00 am - 5:00 pm
Instructors: Belinda Weaver, Leah Roberts, Areej Al-Sheikh, Josh Thia, Paula Andrea Martinez
Helpers: Othmar Korn, James Lefevre, Nicholas Hamilton (Dr Nick), Stephane Guillou, Luen-Hsien Chang, Liz Cooper-Williams
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 and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: This course is being run as a tie-in event for the UQ Winter School in Mathematical and Computational Biology. We particularly encourage postgraduate students and early career researchers to attend and kickstart their digital skills. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: The Boardroom, St. Leo's College, College Road, St Lucia QLD 4067. Get directions with OpenStreetMap or Google Maps.
Requirements: You will need to bring a laptop with the specific software packages installed as detailed below. We will also offer a cloud option. You are also required to abide by Software Carpentry's Code of Conduct.
Contact: Please mail b.weaver@uq.edu.au for more information.
Schedule
Surveys
Please be sure to complete these surveys before and after the workshop.
Day 1
| 08:30 | Setting up and software installation help |
| 09:00 | Automating tasks with the Unix shell |
| 10:30 | Morning tea |
| 11:00 | Automating tasks with the Unix shell |
| 12:30 | Lunch break |
| 13:30 | Introduction to R |
| 15:00 | Afternoon tea |
| 15:30 | Rstudio, R help |
| 16:45 | Wrap-up |
Day 2
| 08:30 | Setting up and software installation help |
| 09:00 | Version control with Git - Intro |
| 10:30 | Morning tea |
| 11:00 | Version control with Git - Collaboration |
| 12:30 | Lunch break |
| 13:30 | Graphing and using packages in R |
| 15:00 | Afternoon tea |
| 15:30 | Making your own R scripts |
| 16:45 | Wrap-up |
Etherpad: http://pad.software-carpentry.org/uqws-r.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Syllabus
The Unix Shell
- Files and directories
- History and tab completion
- Pipes and redirection
- Looping over files
- Creating and running shell scripts
- Finding things
- Reference...
Programming in R
- Working with vectors and data frames
- Reading and plotting data
- Creating and using functions
- Loops and conditionals
- Using R from the command line
- Reference...
Version Control with Git
- Creating a repository
- Recording changes to files:
add,commit, ... - Viewing changes:
status,diff, ... - Ignoring files
- Working on the web:
clone,pull,push, ... - Resolving conflicts
- Open licenses
- Where to host work, and why
- Reference...
Wireless Internet Access
You will be able to access wireless internet through eduroam - please check your institution's IT support pages for how to connect. Try to connect to eduroam at your institution before you come to the workshop as this saves a lot of time.
Setup Option 1: Local Installation On Your Laptop
As an alternative to the DIT4C cloud option, you can install the software locally on your machine, using the instructions below. If you are having issues, please arrive before 9:00am to get your install checked by a helper.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
The Bash Shell
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Windows
- Download the Git for Windows installer.
- Run the installer and follow the steps bellow:
- Click on "Next".
- Click on "Next".
- Click on "Next".
- Click on "Next".
- Click on "Next".
- Select "Use Git from the Windows Command Prompt" and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
- Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
- Select "Use Windows' default console window" and click on "Next".
- Click on "Next".
- Click on "Finish".
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. 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 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
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 (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
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.
Text Editor
When you're writing code, it's nice to have a text editor that is
optimised for writing code, with features like automatic
color-coding of key words. The default text editor on Mac OS X and
Linux is usually set to Vim, which is not famous for being
intuitive. if you accidentally find yourself stuck in it, try
typing the escape key, followed by :q! (colon, lower-case 'q',
exclamation mark), then hitting Return to return to the shell.
Windows
nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
Mac OS X
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
Linux
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
R
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use 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.
Setup Option 2: The DIT4C cloud
We have a cloud based environment available with all the software needed for the workshop pre installed. For this option to work, you will need to setup eduroam (differs for each institution) so you have a working wireless internet connection. Please check you can connect via eduroam before you come to the workshop as this will save time.
We'll give instructions on how to connect to this on the day of the workshop.