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#

ModelCompartmentsUse CaseSIRS, I, RDiseases with lifelong immunitySEIRS, E, I, RDiseases with latent periodSEISS, E, IDiseases with temporary immunitySISS, IDiseases with no immunitySIS, IFatal diseasesCustomUser-definedSpecialized 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)