An introduction to R for plant pathologists written by Drs. Sydney E. Everhart and Zhian N. Kamvar

This repository is intended to serve as an additional resource for short workshops given at Univeristy of Nebraska and The 2017 North-Central American Phytopathological Society Meeting. The source code can be found at


This introduction to R is designed to be a companion to a workshop lasting 3 hours introducing plant pathologists to the basics of R by using a real world stripe rust example.


As a result of taking this workshop you should be able to:

  • find, download, and load necessary packages for analysis
  • load tabular data into R
  • understand the basics of data manipulation in R
  • know what a data frame, vector, and function are
  • summarize data
  • visualize data
  • troubleshoot commmon problems


This website is meant to serve as a companion to the workshop. The pages located in the Workshop tab are rendered versions of R scripts located in the top level of As the workshop is designed to be interactive where the participants are given some control over what direction we should take the analyses, the scripts here are only to serve as guidelines.

These scripts follow these conventions:

  • R code is presented how it would appear in the R console with the first line prefixed with > and subsequent lines prefixed with +. The intent is to encourage the user to type the commands instead of copy and paste.
  • There will be instances where the command is a stop() command. These are points in the workshop where we stop the participants and ask them to talk amongst themselves, take a short survey, or find information using R’s help function.

The website located at can be build via the make program:

make clean # run this to build the site from scratch

Note: if the is changed, make will force-update the index.Rmd and in turn force update the corresponding HTML.

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