Emerson M. Del Ponte


R for Plant Disease Epidemiology (R4PDE) is a book project in the early stages of development. It is based on the teaching notes from my graduate course, FIP 602 - Plant Disease Epidemiology, which is offered every year for students in the Graduate Program in Plant Pathology of the Universidade Federal de Viçosa.

This book is for those interested in studying and modelling plant disease epidemics using R. It provides context and showcases various methods for describing, visualizing and analyzing epidemic data collected over time and/or space. Users should have have a minimum level of knowledge in R to run the examples.

This book is not meant to teach data science using R, as there are already excellent books such as R for data science. If you read Portuguese (as many of the students of my course), I highly recommend Análises Ecológicas no R and Software R para avaliação de dados experimentais as excellent resources for learning R (and also statistics with R).

Throughout the book, I use several general and a few specific R packages to conduct the most common analysis of plant disease epidemiology data, particularly epifitter and epiphy. In most cases, I use data and reproduce some of the analyses shown in the book The study of Plant Disease Epidemics (Madden et al. 2017).

Please note that this is a work in progress, meaning that it is frequently updated and edited. This website is free to use, and is licensed under a Creative Commons licence. The codes for reproducing all analyses shown here are available on GitHub. There are currently no plans to publish a physical copy of the book, but I may consider it in the future as the book takes shape. This website is hosted by https://www.netlify.com/.

R4PDE follows a Contributor Code of Conduct. By contributing to this book, you agree to abide by its terms.


To those who have contributed fixes and improvements via pull request or other form of contact: Adam Sparks (@adamhsparks), Remco Stam (@remco-stam)