comomodels

The goal of comomodels is to provide pedagogical materials, chiefly a series of transmission dynamics models of increasing complexity, for understanding the spread of COVID-19. The Susceptible-Exposed-Infectious-Recovered-Dead (SEIRD) model is the basis of all the models included in the package. The SEIRD model is extended to model different age groups, groups of varying infectiousness, vaccination, distinct meta-populations amongst other areas. The schematic figure below shows the various models in the comomodels package.

The currently available models include:

1. SEIRD model.
2. SEIaImIsRD model - an SEIRD model with groups of varying infectiousness. Here, we include asymptomatic, mildly symptomatic and severely ill groups.
3. SEIRDV model - an SEIRD model including vaccinated compartments.
4. SEIRD_BD model - an SEIRD model including births and natural deaths and waning natural immunity.
5. SEIRD_RU model - two linked SEIRD models used to represent two meta-populations, which here we label (and parameterise) as rural and urban populations.
6. SEIRDAge model - an SEIRD model stratified by age, allowing intermixing across ages.
7. SEIRDVAge model - an age-stratified SEIRD model allowing vaccination of different age groups.
8. SEIRDNPIAge model - an SEIRD model accounting for non-pharmaceutical interventions, such as self-isolation.

Installation

The development version of comomodels can be installed from GitHub with:

# install.packages("devtools")
devtools::install_github("Como-DTC-Collaboration/como-models")

Example

There are a series of vignettes, available here, which each provide tutorials for a given model.