## Tutorials

- Tutorial 0: Introduction to R Studio - provides an introduction to the user interface
- Tutorial 1: Introduction to R and its quirks
- Tutorial 2: More on Vectors, Data Frames, and Functions
- Tutorial 3: Probability Distributions and Control Structures
- Tutorial 4: Visualizing Infectious Disease Data in R
- Tutorial 5: Data cleaning and management in R

## ICI3D R package

- This package contains interactive tutorials used at the MMED and DAIDD Clinics; to install, run the following lines of code from the R or Rstudio command line:

## Labs

- Lab 1: ODE models in R
- Lab 2: Consequences of heterogeneity
- Download data file
- Note that a newer version of this tutorial is also available through the ICI3D R package. To get started, run the following command at the R Studio command line (after installing the ICI3D package):

- Lab 3: Study Design in Epidemiology lab
- Lab 4: Study Design for Clinical Trials
- Lab 5: Introduction to Likelihood
- Lab 6: MLE fitting of a dynamic model
- Lab 7: MCMC fitting of a binomial distribution
- Lab 8: MCMC fitting of a dynamic model
**Note:**Download this file to avoid having to wait for long MCMC chains to be sampled.

## Exercises and Examples

- Exercise 1: Basic stochastic simulation models - Stochastic spillover
- Exercise 2: Basic stochastic simulation models - Demographic stochasticity
- Stochastic SIR Example - Gillespie Algorithm
- Stochastic SIR Example - Chain Binomial