Overview

A list of resources broadly related to the DSAIDE package and infectious disease modeling (in R). These are resources I’m aware of, many others like exist. Let me know if I’m missing anything.

Other packages by our group

  • A ‘companion’ package to DSAIDE, called Dynamical Systems Approaches for Immune Respone Modeling (DSAIRM), focuses on models for analyzing with-host infection dynamics. It has the same structure as DSAIDE. See the DSAIRM site for more information.

  • A new package (not yet on CRAN) called modelbuilder lets you build and analyze your own compartmental models (ODE, discrete time or stochastic) without having to write code. The package should be working but it’s still in development and some functionality is not there. Check it out and use at your own risk here.

ID modeling R packages

  • idmodelr by Sam Abbott. Many basic compartmental (SIR type) models, a little bit of coding is required. He also has a list of related resources, which - not surprisingly - has a lot of overlap with the information on this page.

  • shinySIR by Sinead Morris. Exploration of several SIR-type models through Shiny. Doesn’t have the documentation of DSAIDE, but has some models not in DSAIDE.

ID modeling books

To come

ID modeling courses

To come

ID modeling websites

epirecipes - a cookbook of ID epi models.