Dalhousie University

Kenneth C. Rowe Management Building, Room 1014
Jul 14-15, 2014
8:00/9:00 am - 6:00/5:00 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. A substantial focus of the workshop will be on improving programming skills in R, but will also include topics on 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, Gavin Simpson, Ross Dickson

Helpers: Daniel Morrison

Who: The bootcamp is targeted at postgraduate students and other researchers in Biology and Oceanography. Please note that this is not an introductory R course and in order to get the most out of the bootcamp, attendees should have at least a basic knowledge of programming in R. However, please don't let that scare you off - if you'd like to attend but have never used R before, working through the online material covered in 'Day 1' of the NiceR code 'Introduction to R' will get you up to speed!

Where: Kenneth C. Rowe Management Building, Room 1014. Get directions with OpenStreetMap or Google Maps.

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

Contact: Please mail diego.barneche@mq.edu.au for more information.


Schedule

Day 1

08:00 - 08:30 Introduction + Rstudio
08:30 - 11:00 Functions
11:00 Lunch break
13:00 - 14:00 Project setup
14:00 - 15:30 Repeating things (plyr)
15:30 - 15:45 Tea break
15:45 - 17:00 Repeating things (loops)
17:00 Wrap-up

Day 2

09:00 - 10:00 Testing
10:00 - 11:00 Basic shell scripting
11:00 Lunch break
13:00 - 15:00 Version control with git
15:00 - 15:15 Tea break
15:15 - 16:00 Git workflows
16:00 - 17:00 Reproducible research with knitr
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

Editor

When you're writing code, it's nice to have a text editor that is optimized 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.

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.

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).

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.