Epigrass Creator

Create Epigrass epidemiological models through step-by-step guided specification. Build metapopulation models (SIR, SEIR, SEIS, SIS, SI) with geographic networks. Supports GeoPackage import for real-world spatial data.

Epigrass Creator Skill

Create epidemiological metapopulation models using Epigrass through an interactive, step-by-step wizard.

What is Epigrass?

Epigrass (Epidemiological Geo-referenced Analysis and Simulation System) is a Python library for simulating disease spread across geographic networks.

Supported Models

Model	Compartments	Use Case
SIR	S, I, R	Diseases with lifelong immunity
SEIR	S, E, I, R	Diseases with latent period
SEIS	S, E, I	Diseases with temporary immunity
SIS	S, I	Diseases with no immunity
SI	S, I	Fatal diseases
Custom	User-defined	Specialized scenarios

Workflow (5 Steps)

1. Model Selection - Choose model type
2. Site Definition - Define geographic locations (manual, grid, cities, or GeoPackage import)
3. Parameters - Configure epidemiological parameters
4. Network - Define connections between sites
5. Simulation - Set simulation settings and generate files

GeoPackage Support

Import sites directly from GeoPackage (.gpkg) files:

• Supports any geospatial vector data
• Automatic coordinate extraction
• Column mapping for name, population, geocode
• Works with municipal boundaries, health regions, etc.

Requirements: pip install geopandas (or fiona as fallback)

Usage Examples

text

User: Create a dengue model for Brazilian cities
→ Wizard guides through SEIR selection, city list, parameters

User: Build SIR model with 10x10 grid
→ Wizard creates synthetic network

User: Custom model with hospitalization
→ Wizard collects compartments and transitions

Output

• model.epg - Epigrass script
• sites.csv - Site/node data
• edges.csv - Edge/connection data
• model_spec.json - Full specification

Requirements

• Python 3.8+
• epigrass (pip install epigrass)