University of Sydney

Law School Seminar Room 444 (upstairs from the Law School Bar)
Oct 31-Nov 1, 2014
9:00 am - 5:00 pm

General Information

This intensive 2-day Software Carpentry bootcamp will introduce attendees to a range of computing skills aimed at making them more productive and efficient in their work. This will include an introduction to R. It is not designed to teach students to calculate specific statistics in R (although a few basic examples will be covered), rather it is mainly about better coding practices that one should be able to apply to different programming environments. The bootcamp will also cover version control, using the shell, and reproducible research. Short tutorials will alternate with hands-on practical exercises. Participants will be encouraged both to help one another, and to apply what they have learned to their own research problems during and between sessions.

Instructors: Diego Barneche, Philipp Bayer, Dan Warren

Helpers: Sarah McIntyre, Steson Lo

Should you sign up? The bootcamp is targeted at postgraduate students and other researchers in Psychology. No previous programming experience is required. However, most students are likely to have a bit of programming experience, if not in a proper language, then at least with scripting as in SPSS or HTML, which will affect the pace of the instruction. We therefore recommend that if you have no programming experience you work through the online material covered in 'Day 1' of the NiceR code 'Introduction to R'.

Where: Law School Seminar Room 444 (upstairs from the Law School Bar). Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Content contact: For more information about the content, email diego.barneche@mq.edu.au

Host contact: For information about practicalities and attendance, email alex.holcombe@sydney.edu.au


Schedule

Friday, 31 October

09:00 - 10:15 Introduction to R + Rstudio
10:15 - 10:30 Tea break
10:30 - 12:15 Functions
12:15 - 12:30 Project setup
12:30 - 13:00 Control flow (conditional statements)
13:00 - 14:00 Lunch break
14:00 - 15:30 Control flow (loops)
15:30 - 15:45 Tea break
15:45 - 16:45 Repeating things (plyr)
16:45 - 17:00 Wrap-up

Saturday, 1 November

09:00 - 10:15 Basic shell scripting
10:15 - 10:30 Tea break
10:30 - 12:00 Version control with git
12:00 - 13:00 Lunch break
13:00 - 15:00 Introduction to GitHub + exercises
15:00 - 15:15 Tea break
15:15 - 16:45 Reproducible research with knitr
16:45 - 17:00 Wrap-up

Setup

To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.

Overview

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

Git

Git is a state-of-the-art version control system. It 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.

Windows

Git Bash

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

Editor

Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.

R

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

Mac OS X

Bash

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.

Editor

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Git

Install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.

R

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

Linux

Bash

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

If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get or yum).

Editor

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

R

You can download the binary files for your distribution from CRAN. Or you can use your package manager, e.g. for Debian/Ubuntu run apt-get install r-base or yum install R. Also, please install the RStudio IDE.