Julia packages for building compartmental epidemic models by algebraic composition (Libkind et al. 2023) and fitting them to surveillance data.
| Package | What it does |
|---|---|
| AlgebraicEpiMech | Builds models as typed Petri nets and composes them: stratification and strain structure by pullback, observation delay chains by pushout. Any composed net is an ODE vector field. |
| ConfigurableEpi | Turns a net into a stochastic state-space model with latent drivers and an observation model, fits it to a count series with filtering methods, and forecasts. |
Documentation: https://cdcgov.github.io/AlgebraicEpiModels
The packages need Julia 1.11 or later and are not yet registered. Add them from GitHub, AlgebraicEpiMech first:
using Pkg
Pkg.add(url = "https://github.com/CDCgov/AlgebraicEpiModels", subdir = "AlgebraicEpiMech")
Pkg.add(url = "https://github.com/CDCgov/AlgebraicEpiModels", subdir = "ConfigurableEpi")See Getting started for a first model and fit, and the examples for more.
Common tasks are recipes in the justfile, e.g. just test AlgebraicEpiMech and just docs-build.
The documentation site is built from docs/; see Maintaining the docs for how the API and example pages are generated.
- Sam Brand (USI1)
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