index.qmd

# Welcome {.unnumbered}

**R for Plant Disease Epidemiology** (R4PDE) is a dynamic online book 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](http://www.dfp.ufv.br/grad/) at Universidade Federal de Viçosa.

Designed for those passionate about studying and modeling plant disease epidemics with [R](https://www.r-project.org/), 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](https://r4ds.had.co.nz/) 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*](https://apsjournals.apsnet.org/doi/book/10.1094/9780890545058) [@madden2007], 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}](https://alvesks.github.io/epifitter/) and [{epiphy}](https://chgigot.github.io/epiphy/), both designed by plant pathologists. In conjunction with this book, a new R package [{r4pde}](https://github.com/emdelponte/r4pde) has been developed and can be installed from GitHub using:

    install.packages("pak")
    pak::pkg_install("Icens")
    pak::pkg_install("emdelponte/r4pde")

This online book is frequently updated and edited. It content is free to use, licensed under a [Creative Commons licence](https://creativecommons.org/licenses/by-nc/4.0/), and the code for all analyses can be found on [GitHub](https://github.com/emdelponte/epidemiology-R). Contributions are subject to a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html), and by contributing, you agree to adhere to its terms.

[R for Plant Disease Epidemiology ](https://r4pde.net/)© 2023 by [Emerson Medeiros Del Ponte](http://emersondelponte.netlify.app/) is licensed under CC BY-NC 4.0 <img src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1" style="margin-left:3px;vertical-align:text-bottom;" width="28"/><img src="https://mirrors.creativecommons.org/presskit/icons/by.svg?ref=chooser-v1" style="margin-left:3px;vertical-align:text-bottom;" width="28"/><img src="https://mirrors.creativecommons.org/presskit/icons/nc.svg?ref=chooser-v1" style="margin-left:3px;vertical-align:text-bottom;" width="28"/>