The Clarke Lab’s R modules

The Clarke Lab’s Introductory R modules were designed for the course Curiosity to Question: Research Design, Data Analysis and Visualization (or CtQ), created and taught by Dr. Julia Clarke at the Jackson School of Geosciences (University of Texas at Austin). This course is focused on honing principles of experimental design (including formulation of target questions and method choice), scientific writing, as well as providing an introduction to tool kits for data analysis and data visualization. Students in the class have independent projects that they complete throughout the course of the semester. The final project of the course is a complete, formatted short manuscript for a scientific journal. Graduate students in the class receive additional training in mentorship and are expected to model leadership in the course.

Part of the class is dedicated to learning comparative statistics in the context of individual projects: students receive basic training on the use of the statistical software R, and use it to analyze the data they collected for their project and present the results described in their final papers. To assist with the teaching of R, instructors in the class have created detailed tutorials and material that present most classic methods and tricks. These tutorials have been compiled in the R Markdown format. Students are expected to read through those modules and execute lines of code themselves to learn how to use the different R functions detailed in those tutorials. Additional links to online resources and example datasets are also provided.

This original material is available as three separate teaching modules, in the R Markdown (executable) and HTML (read only) formats. We recommend that you download all the modules and associated files at once, so that you can put them in a folder on your computer that you can use as your working directory when opening them in R.

Each module ends with exercises that the students are expected to complete and submit to the instructors for the next class. These exercises cover most basic functions shown in the modules, and are to be answered directly in the original script files, in empty code chunks created for that purpose. The answers to the exercises are provided as separate HTML files, and are password-protected. The password can be found in the original modules, so that user first have the opportunity to read through the exercises themselves and come up with their own answers.

All files require the use of R and RStudio, both freely available.

Material to download:

R modules in R Markdown (.Rmd) format

R modules in HTML format

Additional material (needed to execute the Markdown scripts)

Answers of exercises (password needed)

These R modules were designed primarily by Dr. Chad Eliason, Dr. Nick Crouch, Dr. Lucas Legendre, and Dr. Carlos Rodríguez-Saltos.
Exercises designed by Lucas Legendre, Markdown files compiled by Carlos Rodríguez-Saltos.