index.Rmd

---
title: "An applied genomic epidemiological handbook."
author: "Allison Black and Gytis Dudas"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: bookdown::gitbook
documentclass: book
bibliography: [book.bib, packages.bib]
biblio-style: apalike
link-citations: yes
github-repo: alliblk/genepi-book
description: "This is a short guide to the theory and practice of genomic epidemiology, oriented towards viral pathogens."
---

```{r include=FALSE}
# automatically create a bib database for R packages
knitr::write_bib(c(
  .packages(), 'bookdown', 'knitr', 'rmarkdown'
), 'packages.bib')
```

```{r title-page, out.width='90%', fig.asp=.75, fig.align='center', echo=FALSE}
knitr::include_graphics("figures/gytis-tree-title-page.png")
```

```{r eval=FALSE, echo=FALSE}
install.packages("bookdown")
# or the development version
# devtools::install_github("rstudio/bookdown")
```

# Welcome to an applied genomic epidemiological handbook {-}

![](figures/gytis-tree-title-page.png)

This handbook provides a short guide to the theory and practice of viral genomic epidemiology for public health purposes. It is intended to be an open resource - if you feel that this book would be useful to someone, please share it with them. This handbook is almost meant to be "living". If you would like to recommend changes, or if you find errors that should be corrected, or you'd like to see a topic added, please [open an issue in the git repo](https://github.com/alliblk/genepi-book/issues).

This work is licensed as [CC BY-NC](https://creativecommons.org/licenses/).