Introduction to R

Moffitt Cancer Center

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📆 Mondays June 7 - July 19, 2021

⏰ 3:00 pm

🏢 via Zoom (see links below)

💻 Moffitt

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Setup

The course will be hosted through Zoom with video recordings posted on Ponopto after. Links to recorded lectures will be emailed out after class.

Slides

• Introduction and R and Rmarkdown
• Data Manipulation I and II
• Visualization with ggplot
• Statistical testing
• Best practices

Code

Find our live coded notes in notes/ as we commit them.

Questions?

Feel free to ask questions in the GitHub Issues.

Overview

This is a six week course designed to introduce future users to R and Rstudio. We will cover data cleaning using the tidyverse, creating visuals with ggplot, basic statistical analysis and writing documents with Rmarkdown. In the end you should be able to:

• import and manipulate data into different formats
• create new variables and recode existing ones
• plot data using the appropriate figure type
• perform basic statistics
• write Rmarkdown reports

Who is this course designed for?

Have you never written any code in R or any other programming language? Are you familiar with R, but hoping to bulk up your basic skills? Have you used R but are new to the tidyverse framework?

Learning objectives

Introduction to R/Rstudio and Rmarkdown

• Get familiar with the R and Rstudio environment
• Understand basic R code structure (packages, data structures)
• Create and render Rmarkdown documents in multiple formats

Data import and manipulation - Part I

• Import various data types
• Explain the fundamentals of "tidy data" and the tidyverse
• Clean data sets using dplyr verbs

Data manipulation and cleaning - Part II

• Merge data sets
• Transform data

Visualization

• Understand the principles of ggplot2
• Determine appropriate visualizations
• Plot - geom_smooth to see a model over the data

Basic statistics

• ttest, correlation and chisq
• Model data
• Report findings from R output

Final coding project

• Organize projects and name objects in a uniform manner
• Create a reproducible workflow
• Setting up your own R installation

Materials/RStudio Cloud

Materials will be made available on GitHub. If you are using an organization-issued laptop, you may want to verify before you arrive that you can access GitHub.

In this course, we will be using a version of RStudio available online. The class workspace can be accessed here. Please create a user account before the first day of class (or connect with either a GitHub account or Google account).

Schedule and Links

• June 09 - rmarkdown
  • Zoom link
  • Ponopto lecture recording
• June 16 - Data import and wrangling part I
  • Zoom link
  • Ponopto lecture recording
• June 23 - Data import and wrangling part II
  • Zoom link
  • Ponopto lecture recording
• June 30 - Visualizations with ggplot2
  • Zoom link
  • Ponopto lecture recording
• July 14 - Basic statistics
  • Zoom link
  • Ponopto lecture
• July 21 - Best practices
  • Zoom link
  • Ponopto lecture

Instructors

This course is taught by members of Moffitt staff including Jordan Creed, a data analyst in the Department of Health Informatics, Zachary Thompson and Ram Thapa, biostatisticians in the Bioinformatics and Biostatistics Core.

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