ICI3D R tutorials and labs

Overall Repository

You can find all the tutorial materials at the ICI3D/RTutorials reposiory. In addition to the materials below, this will also include historical versions and materials like live and participatory coding sessions.

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

Labs

• Lab 1: ODE models in R
• Lab 2: Consequences of heterogeneity; run ICI3D::heterogeneityTutorial() at the R prompt
  • If you would like to look under the hood, the relevant code is available here.
• 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: Stochastic simulation models - Stochastic spillover
• Exercise 2: Stochastic simulation models - Demographic stochasticity
• Stochastic SIR Example - Gillespie Algorithm
• Stochastic SIR Example - Chain Binomial

Participatory Coding Archive

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)

Pre-2023

• 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)