EPI 501 Dynamics of Infectious Disease (Review)

Table of Contents (reverse chronological)

• Common Error Messages

• Week 7 (March 6, 2017)
  • Final Review [PDF]
  • Contact network models [PDF] | [Code] | [Data]
• Week 4 (February 17, 2017) - Revised 2/16/2017
  • Network models worksheet [PDF] | [Code] | [Data]
• Week 3 (February 10, 2017) — No lab
• Week 2 (February 3, 2017 lab) — Revised 2/3/2017
  • Ebola worksheet [PDF] | [Code]
    • SEIR with case fatality
    • Track total counts and total deaths
    • Effects of time-varying transmission probability
    • R0 and time-varying transmission probability
    • SEIR with time-varying transmission
  • Measles worksheet [PDF] | [Code]
    • Measles SIR
    • Time-steps are arbitrary
    • Chickenpox and mumps
    • Plot multiple things
    • Find max infections
    • Boolean vectors
    • SEIR models
    • Open SEIR models
    • Plotting subsets
    • What is a for-loop
    • How birth/death rate affects I
• Week 1 (January 27, 2017 lab) – Revised 2/1/2017
  • Introduction to ODEs in R [PDF] | [Code]
    • SIR model line-by-line
    • Plotting simulations
    • Make an SI model
    • Make an SIS model
    • Make an SIR with births/deaths
• Week 0 (January 23, 2017)
  • Swirl Tutorial
  • Introduction to R
  • Shiny app for ODE models

Source

You can find the source code along with all class code and PDFs on this project’s GitHub page.