1 Infectious Disease Modelling with Epidemix

1.1 Introduction to models with Epidemix

The Epidemix Shiny App is a R-based online app. It provides an easy interface to run simple epidemiological models without the need for installing or coding in R. Before starting the practical we will have a brief overview.

The interface is divided in two main parts, the inputs panel on the left side and the outputs on the right. The outputs panel shows the model results, either graphically or listed in a downloadable table.

The first decision you need to make is whether to use a generic model or a disease-specific one. At the moment, the only disease-specific models are for Covid-19, Avian flu and African Swine Fever.


The first drop-down Select model type allows you to choose the type of model you want to work with. As you can see in the figure below, there are few model classifications: Deterministic vs. Stochastic and Compartmental (COMP) vs. Individual Based Models (IBM). The third criterion with which these models are described regards the host population structure: homogeneous (all hosts can be in contact equally with each other), heterogeneous (hosts are divided in two groups), metapopulation (hosts are divided in several sub-populations), network (hosts are in contact with a set pre-defined neighbours) and spatial (contacts between hosts depend on their position in space).


In Select infection states to consider you can choose the epidemiological structure of your model, for example including an Exposed (infected but uninfectious) stage or specify if infectious individuals are asymptomatic, symptomatic or both (in this practical we won’t use the asymptomatic). In the plot output the infectious are indicated as Infectious-symptomatic, the exposed as Infected(latent), and the recovered as Recovered-immune.


For any panel, you can click the blue “i” to get a full explanation of the features. See the example for Select infection states to consider.