3 - 4 July 2018
9:45 am - 5 pm
Instructors: Peter Humburg, Adela Sobotkova, James Lawson
Helpers: Beth Signal, Martin Ostrowski, Anastasios Papaioannou
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 intermediate to advanced concepts in R. 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 should be familiar with the basics of R. Take a look at the Software Carpentry Introduction to R to see what is expected.
Where: Room 200, 14 Sir Christopher Ondaatje Avenue, Macquary University. Get directions with OpenStreetMap or Google Maps.
When: 3 - 4 July 2018. Add to your Google Calendar.
Requirements: Participants are assumed to be comfortable using R, at least to the level tought in the Introduction to R. Participants must bring a laptop with a Mac, Linux, or Windows operating system (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 organizers 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 (using contact details below) and we will attempt to provide them.
Contact: Please email resbazsydney@googlegroups.com or peter.humburg@mq.edu.au for more information.
Please be sure to complete these surveys before and after the workshop.
| Before | Pre-workshop survey |
| 09:45 | Advanced R Session 1 |
| 11:00 | Coffee |
| 13:00 | Lunch break |
| 14:00 | Advanced R Session 2 |
| 15:15 | Coffee |
| 16:30 | Wrap-up |
| 17:00 | END |
| 09:45 | Introduction to Shiny |
| 11:00 | Coffee |
| 13:00 | Lunch break |
| 14:00 | Exploring Geospatial Data with R |
| 15:15 | Coffee |
| 16:30 | Wrap-up |
| 16:50 | Post-workshop Survey |
| 17:00 | END |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
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 is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio. It is recommended that you install the latest version of R (version 3.5.0) and RStudio (version 1.1.453).
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
Install R 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 dnf install R). Also, please install the
RStudio IDE.
During the workshop you will use a number of different R packages. Please ensure you have installed the following packages from CRAN.
Open RStudio and enter install.packages(c("data.table", "doParallel", "gapminder", "foreach", "ggplot2", "itertools", "knitr", "plyr", "reshape2", "rgdal", "raster", "sf", "shiny"))
at the R command line. You may be prompted to select a CRAN mirror. Any mirror in the list should work but the ones located
in Australia are likely to provide the fastest downloads.
If you encounter any difficulties with the geospatial packages rgdal, raster, or sf, refer to the OS-specific instructions on prerequisities at the geospatial workshop homepage.
Open RStudio and enter install.packages(c("data.table", "doParallel", "gapminder", "foreach", "ggplot2", "itertools", "knitr", "plyr", "reshape2", "rgdal", "raster", "sf", "shiny"))
at the R command line. You may be prompted to select a CRAN mirror. Any mirror in the list should work but the ones located
in Australia are likely to provide the fastest downloads.
If you encounter any difficulties with the geospatial packages rgdal, raster, or sf, refer to the OS-specific instructions on prerequisities at the geospatial workshop homepage.
You will need *gdal*, *geos* and *proj4* installed on your system before installing the geospacial packages, such as *rgdal* and *sf*. Please allow for plenty of time and follow the instructions on the geospatial workshop homepage to install the prerequisites.
Once you have installed the prerequisits, open RStudio and enter install.packages(c("data.table", "doParallel", "gapminder", "foreach", "ggplot2", "itertools", "knitr", "plyr", "reshape2", "rgdal", "raster", "sf", "shiny"))
at the R command line. You may be prompted to select a CRAN mirror. Any mirror in the list should work but the ones located
in Australia are likely to provide the fastest downloads.