epi-modeling

What problem does it solve?

This Skill helps you transform outbreak data into interpretable epidemic dynamics by building compartmental models, fitting parameters, and estimating the time-varying reproduction number Rt.

Core Features & Use Cases

• Compartmental epidemic modeling: Build SIR, SEIR, and SEIHR (hospitalization) ODE systems and run stiff solvers for outbreak-scale dynamics.
• Parameter fitting & validation: Fit transmission/incubation/recovery parameters to observed incidence using global optimization and return RMSE plus fitted trajectories.
• Rt estimation & sensitivity: Estimate Rt over time using a sliding-window exponential growth approach with serial-interval assumptions, and analyze parameter influence using PRCC.
• Use case: You have daily case counts for a specific region and want a robust SEIR fit, then track whether transmission is trending above or below replacement over time.

Quick Start

Ask the agent to fit an SEIR model to your daily incidence series and return the fitted parameters and an Rt time series with uncertainty bounds.