May 2022
Odum School of Ecology
The 2022 Ecology 8540 Computational Workshops are intensive modules providing students with the skills needed to organize, analyze and visualize data. This repository contains course materials for Module 2: “Data visualization for ecology & epidemiology”
To register: ideas@uga.edu
CRN 63694
Monday, May 23, 9am-5pm
Tuesday, May 24, 9am-5pm
Wednesday, May 25, 9am-12pm
INSTRUCTORS
John Drake (jdrake@uga.edu)
Éric Marty (emarty@uga.edu)
This module presents basic principles and best practices for data visualization in R, with examples drawn from ecology and epidemiology. Topics include visualizing high-dimensional data, mapping, color, interactive visualizations, and workflows for publication-ready figures.
By the end of this module, students should have a familiarity with the basic principles of data visualization. Students should be able to create figures covering a range of chart types and problems in ecology and infectious disease, applying best practices in data visualization.
Students will complete 6 in-class exercises on a range of topics. In addition, students will work in groups to complete one longer project of their choosing. Groups will present completed projects to the class at the end of the course, and receive feedback from their peers.
DAY 1: Monday, May 23
Slide lectures may be downloaded and opened in browser.
09:00 Lecture:
Introduction
09:40 Exercise: Exercise 1: Figure
redesign
10:20 Break
10:30 Lecture: Chart
types
11:10 Exercise: Exercise 2: Time
series
11:50 Wrap-up
12:00 Lunch
01:30 Lecture: Visualizing high-dimensional
data
02:10 Exercise: Exercise 3: High-dimensional
data
02:50 Break
03:00 Group projects
DAY 2: Tuesday, May 24
09:00 Lecture: Aesthetics &
Color
09:40 Exercise: Exercise 4: Reproduction Number
10:20 Break
10:30 Lecture: Graphic
Perception
11:10 Exercise: Exercise 5: Workflows
11:50 Wrap-up
12:00 Lunch
01:30 Lecture:
Mapping
02:10 Exercise: Exercise
6
02:50 Break
03:00 Group projects
DAY 3: Wednesday, May 25
09:00 Group projects
10:50 Break
11:00 Presentation of group projects
https://github.com/CEIDatUGA/ECOL8540-datavis/tree/master/projects
register: ideas@uga.edu
ECOL 8540
CCN: 63694
Step 1. Github credentials
You will need a GitHub account and a Personal Access Token (PAT) with “scope” set to “repo”. If you do not have a GitHub PAT, you can create one as follows:
- Log into GitHub on the web.
- Under your user icon, go to Settings > Developer Settings > Personal Access Tokens
- Click
Generate new token. - Name the token something relevant, click the box next to
repo, set an expiration date if desired, and clickGenerate token. - Copy the token and save it somewhere safe and permanent. You will not be able to look up the token after you close the window.
You will use this token in place of a password during the next step.
Step 2. Log in to the Ecology RStudio Server with your class login and password
https://rstudio.ecology.uga.edu/
Step 3. Clone the class repository into a new R Project:
File > New Project > Version Control > Git
Repository URL: https://github.com/CEIDatUGA/ECOL8540-datavis.git
Click “Browse” to choose or create the directory to put the project in.
When asked, enter your PAT in place of a password.