EpiLPS: a fast and flexible Bayesian tool for near real-time estimation of the time-varying reproduction number

Abstract

The instantaneous reproduction number R(t) is a key metric that provides important insights into an epidemic outbreak. We present a flexible Bayesian approach called EpiLPS (Epidemi-ological modeling with Laplacian-P-splines) for smooth estimation of the epidemic curve and R(t). Computational speed and absence of arbitrary assumptions on smoothing makes EpiLPS an interesting tool for near real-time estimation of the reproduction number. An R software package is available (https://github.com/oswaldogressani).