Pandemic Simulator - Compartmental Models¶
A library of compartmental disease models in the WHO Pandemic Simulator.
For Modelers¶
Describe a model once -- its compartments, the flows between them, and the parameters it takes -- and the framework builds everything else from that description:
- the file the web app reads to build its input forms and store model settings
- the checks that catch a bad or incomplete configuration before a run starts
- a ready-to-run example configuration, filled in with sensible defaults
You can use functions from any of the existing models, or write your
own custom model -- see the
Model Integration Documentation to
get started.
- Parameter Framework Reference -- all available
parameter types, the ParameterSchemaBuilder API, and ValueType options
API Reference¶
| Module | Description |
|---|---|
| Parameter Framework | ParameterSchemaBuilder, ValueType, ParameterDef, and all schema dataclasses |
| Base Model | Model ABC -- the base class all disease models extend |
| Interventions | JAX-compatible intervention functions for modifying transmission rates |
Disease Models¶
| Model | Module | Description |
|---|---|---|
| Novel Respiratory (SEIHDR) | covid_jax_model |
An SEIHDR compartmental model for novel respiratory diseases with age-stratified transmission |
| Novel Respiratory (SEIHR) | covid_jax_model.variants |
An SEIHR compartmental model for novel respiratory diseases with age-stratified transmission |
| Novel Respiratory (SEIDR) | covid_jax_model.variants |
An SEIDR compartmental model for novel respiratory diseases with age-stratified transmission |
| Novel Respiratory (SEIR) | covid_jax_model.variants |
An SEIR compartmental model for novel respiratory diseases with age-stratified transmission |
| Novel Respiratory (SIHDR) | covid_jax_model.variants |
An SIHDR compartmental model for novel respiratory diseases with age-stratified transmission |
| Novel Respiratory (SIHR) | covid_jax_model.variants |
An SIHR compartmental model for novel respiratory diseases with age-stratified transmission |
| Novel Respiratory (SIDR) | covid_jax_model.variants |
An SIDR compartmental model for novel respiratory diseases with age-stratified transmission |
| Age-Stratified SIR (per-age transmission) | age_stratified_sir_model |
An SIR model in which each age group has its own transmission rate, with age mixing through a contact matrix and spatial mixing through a travel matrix. |
| Novel Respiratory (SIR) | covid_jax_model.variants |
An SIR compartmental model for novel respiratory diseases with age-stratified transmission |
| Example SIR | basic_sir_model |
A simple SIR model with frequency-dependent transmission |
| Ebola Virus Disease | ebola_jax_model |
Discrete-time stochastic SEIR model with hospitalisation and funeral transmission, Erlang(2) passage times via linear chain (Li et al. 2019, Getz & Dougherty 2018). |
| Ebola SEI1I2RD | ebola_importation_model |
Ebola SEI(R)I(D)RD model with separate infectious strata for recovering and dying cases, used to estimate importation risk |
| Hantavirus (spatial spillover) | hantavirus_jax_model |
Three-sector (urban / rural-populated / rural-empty) rodent-to-human hantavirus spillover model with explicit human and rodent commuting and residence-by-infection-site case bookkeeping (Cornejo-Donoso et al., PMC10536976). |
| Hantavirus (person-to-person + risk perception) | hantavirus_human_jax_model |
SEIR hantavirus model coupling rodent-to-human spillover with Andes-virus person-to-person transmission and a dynamic risk-perception state that modulates both betas (Gutiérrez Jara & Muñoz Quezada, Medwave 2022). |
| MPOX | mpox_jax_model |
A simple SIR compartmental model for MPOX |
| Respiratory disease with adaptive behavior based on reported (or hospitalized) cases | respxiety_model |
A simple model of a respiratory disease with adaptive behavior determined by the number and rate of change of detected (reported or hospitalized) cases |
| Age-structured SEIcIscR (clinical/subclinical) | wuhan_seir_model |
Age-structured SEIcIscR model of the Wuhan COVID-19 outbreak with clinical and subclinical infectious compartments and contact-matrix mediated transmission. |
| Dengue (4-serotype) | dengue_jax_model |
A 4-serotype vector-borne dengue model with temperature-driven mosquito dynamics |
| Dengue (2-Strain) | dengue_2strain_jax_model |
A two-strain dengue model with seasonal transmission, temporary cross-protective immunity, and antibody-dependent enhancement of secondary infections. |
| Chikungunya SIR Model | chikungunya_sir_model |
A deterministic SIR model of chikungunya transmission with optional NPI and vaccination interventions. |
| Ebola (SEIHFR, Community/Hospital/Burial) — Legrand et al. 2007 | ebola_seihfr_burial_legrand_model |
SEIHFR compartmental model of Ebola virus disease with explicit community, hospital, and traditional-burial transmission routes, fitted to the 1995 DRC and 2000 Uganda outbreaks (Legrand et al., Epidemiol. Infect. 2007). |
| ebola_seihfr_stochastic_lai_v1 | ebola_seihfr_stochastic_lai_v1_model |
Stochastic (chain-binomial tau-leap) SEIHFR model of Ebola virus disease with explicit community, hospital, and traditional-burial transmission routes, based on Legrand et al. (Epidemiol. Infect. 2007). Demographic-noise counterpart of the deterministic ebola_test model. Defaults are the DRC (Kikwit) 1995 preset. |
| Example Disease with Parameter Uncertainty and Custom Equation | example_parameter_uncertainty_custom_model |
A SIR model for an example disease with parameter uncertainty, a custom written equation and a ramped intervention |
| Example Disease with Declarative Parameter Uncertainty | example_parameter_uncertainty_declarative_model |
A SIR model for an example disease with declarative parameter uncertainty |
| Example Disease with Spatial Mobility | example_spatial_mobility_v2_model |
A spatial, age-structured SIR model with selectable inter-zone mobility, contact-matrix age mixing, and a single transmission rate |
| Example Disease with Stochasticity | example_stochastic_model |
A stochastic SIR model for an example disease |
| Measles SEIR calibrated to the 2025 Texas outbreak (Gonzalez-Parra et al.) | measles_seir_calibrated_gonzalezparra_model |
SEIR measles model whose transmission rate is calibrated to the 2025 Texas weekly case series (rising limb) via the dataset input, then simulated forward. The transmission rate is fixed by the data and is not a user input; the latent and infectious periods remain adjustable. |
| Test: COVID-19 Stochastic SIR | test_covid_sir_stochastic |
A simple stochastic SIR model for COVID-19 |
| Test: Klebsiella pneumoniae AMR | test_klebsiella_amr_model |
Compartmental model for ESBL and carbapenem-resistant K. pneumoniae transmission across hospital and community settings (Kachalov et al. 2021) |