Nathan Campus, Griffith University

29th-30th May 2017

8:30-4:30

Instructors: Kim Keogh, Heidi Perrett, Amanda Miotto

Helpers:

To sign up, please register your details here : https://goo.gl/forms/jNGRXhXn1pmY7AIg1

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.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Kessels Rd, Nathan. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.

Contact: Please mail a.miotto@griffith.edu.au for more information.


Schedule

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Day 1

09:00 Introduction to R and R Studio
10:30 Coffee
12:00 Lunch break
13:00 Continue with R and R Studio
14:30 Coffee
16:00 Wrap-up

Day 2

09:00 Introduction to R and R Studio
10:30 Coffee
12:00 Lunch break
13:00 Continue with R and R Studio
14:30 Coffee
16:00 Wrap-up

Syllabus

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...

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.

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.

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

Video Tutorial

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

Mac OS X

Video Tutorial

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.

Lesson R Important links, lessons and data

Lessons online : http://swcarpentry.github.io/r-novice-inflammation/

Data to download: http://swcarpentry.github.io/r-novice-inflammation/files/r-novice-inflammation-data.zip

We are gong to download this directly into RStudio if possible however if you need to download to your computer, use the following...


Please unzip after downloading. If you are in Mac or Linux, you can use the following commands:

Windows: you can download it and move it to the folder you plan on working in, then unzip it by right clicking

Mac:

curl -O http://swcarpentry.github.io/r-novice-inflammation/files/r-novice-inflammation-data.zip

unzip r-novice-inflammation-data.zip

Linux:

wget http://swcarpentry.github.io/r-novice-inflammation/files/r-novice-inflammation-data.zip

unzip r-novice-inflammation-data.zip


If all else fails- ResBaz Cloud

If you have issues with these installations, please arrive to class early and an instructor can assist you in installation. Failing that, available are the ResBaz Cloud that we can use to do this work via a web browser. Please find the site below, log in via the Australia Access Federation then ask an instructor for the password. ResBaz Cloud.