Epidemiology

The concepts that turn a stream of case reports into an understanding of how a pathogen moves through a population. This collection starts with the time intervals that structure transmission — the delays between infection, symptoms, and onward spread — and the modern methods for estimating them from imperfect surveillance data. Each page pairs the biology and notation with worked examples and runnable code in R, Python, and Julia.

Epidemiological delays and intervals

• Epidemiological Intervals and Delays — incubation, latent, and infectious periods; the serial and generation intervals; and how they shape $R_t$
• Fitting Delay Distributions: Truncation and Censoring — estimating delays from real-time data with interval censoring and right truncation

Related quantitative methods

These pages in the Quantitative Methods collection develop the machinery the epidemiology pages build on.

• Compartmental Models (SIR) — the SIR model and $R_0$
• The Effective Reproduction Number and Forecasting
• Survival Analysis — hazards and censoring
• Maximum Likelihood Estimation
• Fitting Dynamic Models to Data