Griffith University
Introduction to R

R for Reproducible Scientific Analysis

Griffith University
Virtual Campus (hosted on Zoom)

15th to 18th June 2020

9:00am-12:30pm

Instructors: Kim Keogh

Helpers: McKenna Buckley, Jacob Dore-Porret

To hear about future classes:

Please complete this form: Interested in Workshops

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: Hosting training virtually via Zoom

When: 15th to 18th June 2020. Add to your Google Calendar.

Requirements: 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).

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 eresearch-support@griffith.edu.au for more information.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct.This document also outlines how to report an incident if needed.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

Before Pre-workshop survey
09:00 Introduction to R and RStudio - Lessons 1-2
10:30 Morning break
10:50 Introduction to R - Lessons 3-5
12:30 END

Day 2

9:00 Introduction to R - Lessons 6-7
10:30 Morning break
10:50 Plotting data using R - Lessons 8
12:30 END

Day 3

09:00 Introduction to R - Lessons 9-10
10:30 Morning break
10:50 Introduction to R - Lessons 11-12
12:30 END

Day 4

09:00 Introduction to R - Lessons 13-14
10:30 Morning break
10:50 Introduction to R - Lessons 15-16
12:15 Wrap-up
12:25 Post-workshop Survey
12:30 END

Lesson Details: R

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

Data to download: https://raw.githubusercontent.com/resbaz/r-novice-gapminder-files/master/data/gapminder-FiveYearData.csv

We are going 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 https://raw.githubusercontent.com/resbaz/r-novice-gapminder-files/master/data/gapminder-FiveYearData.csv

Linux:

wget https://raw.githubusercontent.com/resbaz/r-novice-gapminder-files/master/data/gapminder-FiveYearData.csv



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...
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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.

Video Tutorial

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.

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.