Overview

This page contains material that show how one can modify the underlying functions from the DSAIRM package to tailor the models to specific questions.

Learning Objectives

• Know how to access and modify the DSAIRM simulation functions.
• Understand the general process of posing a research question, the using models to answer it.

Videos and Code

In this 2020 recording, Andreas takes a brief look at one of the underlying DSAIRM simulation functions and explains a bit how they work. There is no code file for this recording.

In this 2021 recording, we do a small toy research project by modifying one of the underlying simulation functions. For background information: During the SISMID workshop, participants were asked to come up with toy research problems that we might be able to explore with a model.

We settled on two ideas. One idea was to explore antibody dependent enhancement (ADE), which Paul described in the Dengue lecture. We decided to use the Basic Virus and Immune Response app from DSAIRM and modify it to explore a mechanism similar to ADE and how it would impact results. The second idea was to explore the impact of different levels of pre-existing antibody immunity (acquired through e.g. infection or vaccination) on size and duration of an infection.

The following video shows the implementation and exploration of those ideas. Code for the different R scripts that goes with the 2021 lecture is available as a zip file here. It’s not exactly the code you see in the video since I cleaned it up and documented it a bit more after the recording. But it runs everything you see in the recording.

Note: As I was cleaning the scripts after the recording, I realized that in Rscript6.R, we called the wrong function. But we had previously sourced the simulate_virusandir_new2.R function under the simulate_virusandir_new.R name. This means things did work (accidentally). In the clean-up scripts, I fixed that, so now the right functions are called.

This 2022 recording shows an example where we use the Extended Bacteria Model app and modify the code to include various additional features. Code for the different R scripts that goes with the lecture is available as a zip file here. It’s not exactly the code you see in the video since we cleaned it up and documented it a bit more after the recording. But it runs everything you see in the recording.