ICI3D R tutorials and labs

Overall Repository

You can find all the materials below in the ICI3D/RTutorials repository. In addition to the materials below, this will also include historical versions and code from participatory coding sessions.

Current tutorials and labs

Tutorials

These are to learn about R, and should be followed in order.

• 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
• Tutorial 5: Data Wrangling

Labs

These are to learn about the meaningful modelling of epidemiological data in R.

• Lab: ODE models in R
• Lab: Introduction to Likelihood
• Lab: An introduction to stochastic simulation models (stochastic `spillover)
• Lab: Consequences of heterogeneity and supplementary functions
• Lab: Maximum likelihood fitting of a dynamic model
• Lab: Introduction to health economics in dynamical modelling
• Lab: Understanding MCMC
• Lab: MCMC fitting of a dynamic model
  • Note: Download this file to avoid having to wait for long MCMC chains to be sampled.

Application-based labs

• Dynamical fever: ICI3D::dynamicalFever()
• Introduction to models and data: HIV in Harare: ICI3D::hivTutorial()

Extra tutorials and labs

• Lab: Study design in epidemiology
• Lab: Study design for clinical trials
• Example: Stochastic SIR model using the Gillespie Algorithm
• Example: Stochastic SIR model using the Chain Binomial Algorithm

Participatory Coding Archive

2025

• Participatory Coding (Dynamic modeling) 2025 - (Jonathan Dushoff) - Code from session
• Participatory coding (Stochastic model) 2025 - Carl Pearson - Code from session

Pre-2023

• Participatory Coding (ODE model) 2023 - What level of vaccination is needed to eliminate domestic dog rabies in Ouagadougou? (Juliet Pulliam)- Code from session
• Participatory Coding (Gillespie model) (Carl - Code from session)
• Participatory Coding (Dynamic modeling) 2018 - What level of rabies vaccination is necessary to eliminate rabies in Tanzanian dogs?
  • Deterministic model (Difference equations) (Carl Pearson) - Code from session
• Participatory Coding (Dynamic modeling) 2018 - What level of rabies vaccination is necessary to eliminate rabies in Tanzanian dogs?
  • Deterministic model (Difference equations) (Carl Pearson) - Code from session
  • Stochastic model (Chain binomial SEIV) (Carl Pearson) - Code from session
• Participatory Coding (Sampling Var & Study Design) 2018 - Is aidamycin superior to cotrim for treating malaria (under construction)?
  • Single trial
  • Many trials
• Sampling Var & Study Design additional example 2018 - Does vaccinating schoolchildren protect elders from clinical influenza (cluster RCT)?
  • Single trial
  • Many trials
  • A range of protection assumptions
  • Worrying about village-level variance
• Participatory Coding (Sampling Var & Study Design) 2017 - How does village-level ITN coverage affect village-level clinical malaria incidence?
• Participatory Coding (Dynamic Modeling) 2017 - What level of rabies vaccination is necessary to eliminate rabies in Tanzanian dogs?
• Participatory Coding (Dynamic Modeling) 2016 - How does diabetes prevalence affect active TB prevalence (or incidence)?
• Participatory Coding (Sampling Var & Study Design) 2016 - Does recent travel affect prevalence of active TB amongst an immigrant population?
• Participatory Coding 2015 - Does HIV status affect TB incidence rate?
• Participatory Coding 2015 - Can XDR TB invade a population? (didn’t get to XDR yet, but have a working TB model with treatment)