Introduction to infectious disease modeling

Slides: https://www.andreashandel.com/presentations/

Andreas Handel

2023-10-24

How do we do science?

Dilbert

How do we get data?

https://phdcomics.com/

Experimental studies

  • The approach used in almost all bench/lab sciences.
  • Clinical trials in Public Health and Medicine.
  • Potentially most powerful because we have most control.
  • Not always possible.

Observational studies

  • Widely used in Public Health and other areas (e.g., Sociology, Economics, Geology).
  • Not as powerful as experimental studies.
  • Often the only option.

Jim Borgman

Simulation/modeling studies

  • Computer models can represent a real system.
  • Simulated data is not as good as real data.
  • Often the only option.

https://xkcd.com/

Modeling definition

  • The term modeling usually means (in science) the description and analysis of a system using mathematical or computational models.
  • Many different types of modeling approaches exist. Simulation models are one type (with many subtypes).

This one.

Not this

Simulation modeling areas

Source: NOAA

  • Weather forecasting.
  • Simulations of man-made, engineered system.
  • Predicting the economy.
  • Infectious disease transmission.

Infectious disease Simulation models

Computer models for some scenario (e.g. the spread of flu or COVID in the US):

  • Understand what is going on
  • Make forecasts
  • Predict the impact of interventions

Germann et al 2006 PNAS

Models and Reality

  • Every model is a simplification of the real system.
  • It needs to include the details that are important to answer the question of interest.

Simple simulation model (SIR model)

This model tracks individuals (humans or animals) in 3 states, susceptible, infected/infectious and recovered/removed. It is called the SIR model.

Using an SIR-type model

Using an SIR-type model

CDC forecasting

https://covid19forecasthub.org/

Learning simulation modeling

  • It takes time to learn how to build, use and interpret models.
  • One generally needs to write code to build simulation models.

Markus Spiske on Unsplash

DSAIDE R package

  • Software that can teach uses of simulation modeling.
  • Does not require any coding.
  • Allows for active/hands-on learning.

DASIDE

Try for yourself

  • Go to https://shiny.ovpr.uga.edu/DSAIDE/
  • Choose the “Basic SIR Model” app.
  • Play around and explore.

Summary/Questions

  • DSAIDE website: https://ahgroup.github.io/DSAIDE/
  • Slides: https://www.andreashandel.com/presentations/

PhD Comics