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Stellenbosch University

May 14-15, 2015

9:00 am - 5:00 pm

Instructors: Laurent Gatto (remote), David Merand, Anelda van der Walt

Helpers: Raïssa Philibert, Beatrix Coetzee, Rachelle Bester, Maia Lesosky

General Information

We would like to invite postgraduate students and researchers to participate in a Software Carpentry workshop hosted by the Department of Genetics at Stellenbosch University and Talarify.

Software Carpentry's mission is to teach researchers basic computational skills to help them get more research done in less time and with less pain. This introductory level hands-on workshop will cover basic concepts and practices in using R for data analysis, including basic data structures, writing functions, running data analysis on multiple datasets and authoring reproducible documents.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: The workshop is targeted at life sciences postgraduate students and researchers, with limited or no prior experience in R. Participants have to be affiliated with Stellenbosch University. There are only 30 places available

Where: Den Bosch, 37 Victoria Street, Stellenbosch. Get directions with OpenStreetMap or Google Maps. Den Bosch is behind the offices of the Centre for Student Counselling and Development in Victoria Street.

Cost: R500 registration fee.


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.


To be updated.

Day 1

8:30 Coffee & Assistance with setting up laptops
9:00 Introduction - everyone
9:30 Etherpad, RStudio, Getting help
10:30 Tea break
11:00 Data types & Data structures
12:30 Lunch
13:30 Analyzing patient data
15:00 Tea break
15:30 Creating Functions
16:30 Github Demonstration
17:00 Wrap-up and close

Day 2

8:30 Coffee
9:00 Analysing multiple data sets
10:30 Tea time
11:00 Making choices
12:30 Lunch
13:30 Visualisation
15:00 Tea time
15:30 Reproducible research (Markdown & knitr)
17:00 Wrap-up and close

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

Course material: Download the zip archive, extract the content and open the index.html file.


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
  • R authoring: Rmarkdown and knitr
  • Reference...

Demonstration: Version Control with Git and GitHub

  • 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...


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 use RStudio.


Install R version 3.2 by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.

Mac OS X

Install R version 3.2 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, but do check that you have verison 3.2). Also, please install the RStudio IDE.