ResBaz 2017 - R

July 3-4, 2017

9:00 am - 4:30 pm

Instructors: Ghulam Murtaza, Adela Sobotkova, Richard Miller

Helpers: Colin Navin, Ingrid Tarr

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. 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: Dr Chau Chak Wing Building, Building 8, University of Technology, Sydney. Get directions with OpenStreetMap or Google Maps.

When: July 3-4, 2017. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They are also required to abide by Software Carpentry's Code of Conduct. Participants who are not from UTS should ensure that they can connect to the Eduroam wireless network. If you are not sure about how to connect to Eduroam, please consult your local IT department for assistance.

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 email ghulam.murtaza@intersect.org.au , adela.sobotkova@mq.edu.au or richard.miller@mq.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 - 09:20 Acknowledgement of country and Welcome (Auditorium)
09:20 - 11:00 Automating tasks with the Unix shell
11:00 - 11:20 Coffee
11:20 - 13:00 Automating tasks with the Unix shell (cont.)
13:00 - 14:00 Lunch break
14:00 - 15:00 Building programs with R
15:00 - 15:20 Coffee
15:20 - 17:00 Building programs with R (cont.)
17:00 Wrap-up

Day 2

09:00 - 09:40 Keystory: Charmaine Tam (Lecture Theatre)
09:40 - 11:00 Building programs with R (cont.)
11:00 - 11:20 Coffee
11:20 - 13:00 Building Programs with R (cont.)
13:00 - 14:00 Lunch break
14:00 - 15:00 Version control with Git
15:00 - 15:20 Coffee
15:20 - 17:00 Version control with Git (cont.
17:00 Wrap-up

We will use this collaborative document 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...

Setup

This workshop will be taught using NeCTAR Virtual Machines and each participant will be given complete access to one machine. Instructions on accessing the virtual machines will be provided in the workshop.

All participants should ensure that they can access the internet from UTS. If you do not have a UTS account, please make sure you can connect to the internet through Eduroam. Consult your local IT department for assistance.