EpiEstim

EpiEstim estimates time-varying reproduction numbers (R) from incidence data to quantify pathogen transmissibility during infectious disease outbreaks.

Key Features:

• Time-Dependent Reproduction Number Estimation: EpiEstim calculates the expected number of secondary cases generated by each infected individual over time.
• Data Utilization: The tool leverages observed new case data and serial interval distributions to estimate R.
• Distinguishing Transmission Sources: EpiEstim differentiates between locally transmitted cases and imported cases for precise inference of transmissibility.
• Real-Time Data Integration: It incorporates current observations of the serial interval to update estimates promptly.
• Uncertainty Quantification: It provides R estimates together with associated uncertainty measures.

Scientific Applications:

• Outbreak Analysis: EpiEstim has been applied to datasets from H1N1 influenza, Ebola virus disease, and Middle-East Respiratory Syndrome to estimate time-varying transmissibility.

Methodology:

Estimation of time-varying R from observed new case data and serial interval distributions, distinguishing imported versus local cases, integrating current serial interval observations, and reporting associated uncertainty in the estimates.