ICI3D Tutorials

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:

install.packages('remotes') # if not already installed
remotes::install_github('ICI3D/ici3d-pkg') # BEFORE RUNNING THIS MAKE SURE YOUR R VERSION IS 3.5 OR HIGHER

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  • Note that a newer version of this tutorial is also available through the ICI3D R package.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):

ICI3D::heterogeneityTutorial()

• Lab 3: Study Design in Epidemiology lab
• Lab 4: Study Design for Clinical Trials
  • Download data file
• 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