ICI3D R tutorials and labs
Sixth annual Clinic on Meaningful Modeling of Epidemiological Data
June 1-12, 2015, African Institute for Mathematical Sciences, Muizenberg, Cape Town, RSA
Return to the Main Page.
Return to the Schedule.
Tutorials
- Tutorial 0: Introduction to R Studio - provides an introduction to the user interface (required)
- Tutorial 1: Introduction to R and its quirks (required)
- Tutorial 2: More on Vectors, Data Frames, and Functions (required)
- Tutorial 3: Probability Distributions and Control Structures (required)
- Tutorial 4: Visualizing Infectious Disease Data in R (recommended)
- Tutorial 5: Data cleaning and management in R (recommended)
Labs
- Lab 1: ODE models in R (required)
- Lab 2: Consequences of heterogeneity (required)
- Lab 3: Study Design in Epidemiology lab (recommended for Track A)
- Lab 4: Trachoma elimination example (recommended for Track B)
- Note: This link will take you to a public GitHub repository that houses the tutorial. You should clone the repository to work through the example.
- Lab 5: Introduction to Likelihood (required)
- Lab 6: MLE fitting of a dynamic model (required)
- Lab 7: MCMC fitting of a binomial distribution (required)
- Lab 8: MCMC fitting of a dynamic model (optional)
- Note: Download this file to avoid having to wait for long MCMC chains to be sampled.
Exercises
The ICI3D program is supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number R25GM102149.