A Minimal Book Example
Epibible
Preface
About the Author
1
Introduction to Epidemiology
2
Working with this book
2.1
What is bookdown?
2.2
What is Markdown
2.3
Code snippets
2.4
Other formats in this book
3
Getting Started with R
3.1
Installing R and Rstudio
3.2
Starting to code
4
R fundamentals
4.1
R syntax
4.2
Troubleshooting
4.3
Data structures
4.4
writing scripts
5
Tidyverse
5.1
Wide and tidy data
5.2
Data wrangling using dplyr
5.3
Data visualization using ggplot
6
Working with epidemiological data
6.1
Acessing data
6.2
(Imperfect) epidemiological data
6.3
Case Study 1: Yellow Fever
7
Modelling
7.1
Compartmental models
7.1.1
SIR model in theory
7.1.2
SIR model in R
7.2
Time series - Forecasting
7.3
Using and applying models
8
Communication and sharing of code and data
8.1
Writing code: best practices
8.2
Github
8.3
Reports using Markdown
8.4
Open science
8.5
Communities and forums
8.6
How to use Chat-GPT
9
Recommended Reading
9.1
Recommended textbooks and courses
9.2
Datasources
9.3
Useful packages
References
Published with bookdown
Epibible
Epibible
Sten de Schrijver
2025-08-20
Epibible