SISMID Introduction to R Materials (2024)

This is the GitHub hosting the code and resources for the SISMID 2024 Intro to R Module.

About This Course

Module Summary

This module introduces the R statistical environment, assuming no prior knowledge. It provides a foundation for the use of R for computation in later modules. In addition to discussing basic data management tasks in R, such as reading in data and producing summaries through R scripts, we will also introduce R’s graphics functions, its powerful package system, and simple methods of looping.

Hands-on use of R is a major component of this module; users require a laptop and will use it in all sessions. Examples and exercises will use data drawn from biological and medical applications, including infectious diseases and genetics. Participants require a laptop and will use it in all sessions. Suggested pairing: All later modules.

Prerequisites

This module assumes prior knowledge of basic descriptive statistics and regression modeling consistent with an introductory statistical course.

Before starting the course, students should install the newest version of R (here) and RStudio (here).

Module Content

• Write and use R script.
• Create and use R projects and R Markdown files.
• Read and write data files
• Install and load R packages, and be able to access the help system and other resources to facilitate their use.
• Learn base R syntax
• Perform basic data manipulations (e.g. working with different data types, creating new variables, merging data sets).
• Use R to perform descriptive statistics including graphics.
• Perform basic inferential statistical analyses including regression analysis.
• Write and use R functions, and perform basic programming in R including loops.

Repository file structure:

• README.qmd: controls what shows up here on the GitHub page.
• index.qmd: this is the website homepage.
• schedule.qmd: info on the course schedule and logistics
• references.qmd: any references for the course go in the .bib file and get rendered on this page.
• data directory: contains datasets used in the course and exercises
• exercises: contains R or Rmd files for each of the exercises
• format: contains code to format the website appearance
• images: put static image files here
• modules: all of the modules go here. Each module gets its own folder with an index.qmd page that holds the web page content and a separate document for the slides.
• Everything else is housekeeping files needed for the website.

Built With

• Quarto

Contact

The instructors for this course are Amy Winter and Zane Billings.

Contributing

If you see any issues, please open an Issue or Discussion on the book’s GitHub page. Or, if you know Git, you can open a Pull Request to fix the issue directly, which is even better!

Acknowledgements

• Thanks to Callum Arnold for publishing the source code for a 2023 SISMID module which was the basis for this website!

License

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.