SISMID 2022 Course Materials

Schedule: link here

Background Materials:

Please download R here:

Download R Studio here:

We recommend the Sublime text editor for reviewing R code:

Here is a short R tutorial: tutorial file

Background reading on modeling infectious diseases by Heesterbeek et al: link to paper

Day 1 Materials:

Lecture 1: Intro lecture by Micaela Martinez: link 1 and link 2

Lecture 2: Basic SIR dynamics by Matt Ferrari: link here

R Session 1: Intro to modeling by Tiggy Menkir: link to files (link to updated handout)

Lecture 3: Vaccination & Interventions by Micaela Martinez: link 1 and link 2

Group Assignment: link here

Day 1 Recording: recording 1 and recording 2

Day 2 Materials:

Lecture 4: Heterogeneity in SES lecture by Tiggy Menkir: link here

Lecture 4 background reading: link to paper

Lecture 5: Heterogeneity expanded (age structure and the force of infection) by Matt Ferrari: link here

R Session 2: Heterogeneity and age structure by Deepit Bhatia and Matt Ferrari: link to files

Lecture 6: Parameter Estimation (estimating R0) by Matt Ferrari: link here

R Session 3: Parameter estimation by Deepit Bhatia: link to files

Answer key for Day 2 R sessions: link here

Day 2 Recordings: link here

Day 2 R session updated materials (link here). The updated worksheets and answers address the following student feedback:

  1. General:
    1. Removing Rmd files as they were confusing for many participants to work on
  2. Estimation:
    1. Explicit re-naming of variables in the Niamey data so they are easier to run a regression model with
    2. Removing extraneous information that isn’t needed to work on the exercises
  3. Age Heterogeneity
    1. Removed age transition matrix visualization
    2. Parameter values are consistent across worksheets

Day 3 Materials:

Lecture 7: Confronting models with data by Micaela Martinez: link here

Lecture 8: Stochasticity and Uncertainty lecture by Micaela Martinez and Matt Ferrari: link 1

Day 3 Recording: link here

Additional Materials

An Introduction to Infectious Disease Modeling (link here). Recommended sections include:

Chapter 3 – intro to setting up model equations
Chapter 4.1-4.2 – identifying properties that can be gleaned from early epidemic dynamics
Chapter 4.3 – evaluating long-term dynamics
Chapter 5.1-5.2 & Chapter 7.3-7.4 – age structure; analyzing age trends from data, incorporating age structure in models, and estimating key model parameters when such heterogeneities are present
Chapter 8.1-8.5 – modeling STIs
Chapter 6.1 -6.7 – approaches for incorporating stochasticity

Epidemics: Models and Data using R:

Link to R code for each chapter from the book:

Link to Shiny apps showcasing specific types of models:

Certificates of Completion

Certificates of completion for each module can be downloaded from your dashboard shortly after you complete the online evaluation. Immediately after a module concludes, an evaluation for that module will appear on your dashboard. After you complete the last module in an institute, the evaluation will include evaluation questions for both the module and the overall institute (i.e., proceed through both sets of questions to generate the final certificate of completion).

Certificates are generated through the registration system and, occasionally, names and module titles lose their formatting. If this happens, please email and we will get you a corrected copy.

%d bloggers like this: