R for Plant Disease Epidemiology


Emerson M. Del Ponte


October 23, 2023


R for Plant Disease Epidemiology (R4PDE) is a dynamic online book (with ePub and Docx versions) rooted in the teachings of the annual graduate course, FIP 602 - Plant Disease Epidemiology, a key part of the curriculum in the Graduate Program in Plant Pathology at Universidade Federal de Viçosa.

Designed for those passionate about studying and modeling plant disease epidemics with R, the book offers an exploration of diverse methods for describing, visualizing, and analyzing epidemic data collected over time and space. Readers should ideally have a foundational knowledge of R to best utilize the examples.

However, R4PDE is not a resource for learning data science through R, as there are already well-established books such as R for Data Science for that purpose. This book draws on multiple sources, but in some sections, it utilizes data and replicates (with permission) some of the analyses (presented in SAS codes) from The Study of Plant Disease Epidemics (Madden et al. 2007), a highly recommended textbook for anyone wishing to delve deeply into plant disease epidemiology.

A mix of general and specific R packages are utilized to conduct common plant disease epidemiology data analysis, notably {epifitter} and {epiphy}, both designed by plant pathologists. In conjunction with this book, a new R package {r4pde} has been developed and can be installed from GitHub using:


This online book is frequently updated and edited. It content is free to use, licensed under a Creative Commons licence, and the code for all analyses can be found on GitHub. Contributions are subject to a Contributor Code of Conduct, and by contributing, you agree to adhere to its terms.

R for Plant Disease Epidemiology © 2023 by Emerson Medeiros Del Ponte is licensed under CC BY-NC 4.0